From e01afaf18b5e22f72dedbb0ddf8e9466eeaf7593 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
 <gallardo@informatik.uni-freiburg.de>
Date: Wed, 14 Sep 2022 17:39:50 +0200
Subject: [PATCH 1/4] Update_data

---
 tools/clustalw/macros.xml                     | 124 +++++
 tools/clustalw/rgClustalw.xml                 | 150 +++++-
 .../clustalw/test-data/rgClustal_testin02.dnd |  31 ++
 .../clustalw/test-data/rgClustal_testin03.dnd | 103 ++++
 .../test-data/rgClustal_testin_prot.fasta     | 285 +++++++++++
 .../test-data/rgClustal_testout02.aln         |  44 ++
 .../test-data/rgClustal_testout03.aln         | 458 ++++++++++++++++++
 7 files changed, 1182 insertions(+), 13 deletions(-)
 create mode 100644 tools/clustalw/macros.xml
 create mode 100644 tools/clustalw/test-data/rgClustal_testin02.dnd
 create mode 100644 tools/clustalw/test-data/rgClustal_testin03.dnd
 create mode 100644 tools/clustalw/test-data/rgClustal_testin_prot.fasta
 create mode 100644 tools/clustalw/test-data/rgClustal_testout02.aln
 create mode 100644 tools/clustalw/test-data/rgClustal_testout03.aln

diff --git a/tools/clustalw/macros.xml b/tools/clustalw/macros.xml
new file mode 100644
index 000000000..54df266b3
--- /dev/null
+++ b/tools/clustalw/macros.xml
@@ -0,0 +1,124 @@
+     <macros>
+        <token name="@TOOL_VERSION@">2.1</token>
+        <token name="@VERSION_SUFFIX@">1</token>
+        <xml name="requirements">
+            <requirements>
+                <requirement type="package" version="@TOOL_VERSION@">clustalw</requirement>
+            </requirements>
+        </xml>
+        <xml name="macro_algorithm" token_algorithm="" token_label="" token_default="">
+            <param argument="-@ALGORITHM@" type="select" label="@LABEL@ weigth matrix" help="Default: @DEFAULT@">
+                <yield/>
+            </param>
+        </xml>
+        <xml name="macro_multiple" token_multiple="" token_label="" token_default="">
+            <param argument="-@MULTIPLE@" type="select" label="@LABEL@ weigth matrix" help="Default: @DEFAULT@">
+                <yield/>
+            </param>
+        </xml>
+       <xml name="macro_options" token_algorithm="" token_multiple="" token_label="" token_default="">
+            <conditional name="algorithm_conditional">
+                <param name="selector" type="select" label="Algorithm for the alignment guide tree" help="Default: slow">
+                    <option value="">Slow: dynamic programming (accurate)</option>
+                    <option value="-QUICKTREE">Fast: method of Wilbur and Lipman (approximate)</option>
+                </param>
+                <when value="">
+                    <section name="slow_pairwise_alignments" title="Slow pairwise alignments options">
+                        <expand macro="macro_algorithm" algorithm="@ALGORITHM@" label="@LABEL@" default="@DEFAULT@">
+                            <yield/>
+                        </expand>
+                        <param argument="-PWGAPOPEN" type="integer" min="0" optional="true" label="Gap opening penalty" help="Default: 10" />
+                        <param argument="-PWGAPEXT" type="float" min="0" optional="true" label="Gap extension penalty" help="Default: 0.1" />
+                    </section>
+                </when>
+                <when value="-QUICKTREE">
+                    <section name="fast_pairwise_alignments" title="Fast pairwise alignments options">
+                        <param argument="-KTUPLE" type="integer" min="0" optional="true" label="Word size" 
+                            help="Size of exactly matching fragment that is used. Increase for speed, decrease for sensitivity. Maximum value for proteins is 2, and for DNA 4.Default: 1" />
+                        <param argument="-TOPDIAGS" type="integer" min="0" optional="true" label="Number of best diagonals" 
+                            help="Number of k-tuple matches on each diagonal. Decrease for speed; increase for sensitivity. Default: 5" />
+                        <param argument="-WINDOW" type="integer" min="0" optional="true" label="Window length"
+                            help="This is the number of diagonals around each of the best diagonals that will be used. Decrease for speed; increase for sensitivity. Default: 5" />
+                        <param argument="-PAIRGAP" type="integer" min="0" optional="true" label="Gap penalty" 
+                            help="Fast pairwise alignment gap penalty for each gap created. Default: 3" />
+                        <param argument="-SCORE" type="select" label="Score type" help="Score type to output. Default: percent">
+                            <option value="PERCENT">Percent</option>
+                            <option value="ABSOLUTE">Absolute</option>
+                        </param>
+                    </section>
+                </when>
+            </conditional>
+            <section name="multiple_alignments" title="Multiple alignments options">
+                <expand macro="macro_multiple" multiple="@MULTIPLE@" label="@LABEL@" default="@DEFAULT@">
+                    <yield/>
+                </expand>
+                <param argument="-GAPOPEN" type="integer" min="0" optional="true" label="Gap opening penalty" help="Default: 10" />
+                <param argument="-GAPEXT" type="float" min="0" optional="true" label="Gap extension penalty" help="Default: 0.2" />
+                <param argument="-ENDGAPS" type="boolean" truevalue="-ENDGAPS" falsevalue="" checked="false" label="End gap separation penalty" 
+                    help="End gap separation treats end gaps just like internal gaps for the purposes of avoiding gaps that are too close. If you turn this off, end gaps will be ignored for this purpose. 
+                        This is useful when you wish to align fragments where the end gaps are not biologically meaningful" />
+                <param argument="-GAPDIST" type="integer" min="0" optional="true" label="Gap separation penalty range" 
+                    help="Gap separation distance tries to decrease the chances of gaps being too close to each other. Gaps that are less than this distance apart are penalised more than other gaps. 
+                        This does not prevent close gaps; it makes them less frequent, promoting a block-like appearance of the alignment" />
+                <param argument="-NOPGAP" type="boolean" truevalue="-NOPGAP" falsevalue="" checked="false" label="Residue specific penalties" 
+                    help="Residue specific penalties are amino acid specific gap penalties that reduce or increase the gap opening penalties at each position in the alignment or sequence. As an example, 
+                        positions that are rich in glycine are more likely to have an adjacent gap than positions that are rich in valine" />
+                <param argument="-NOHGAP" type="boolean" truevalue="-NOHGAP" falsevalue="" checked="false" label="Hydrophilic gaps" help="Hydrophilic gap penalties are used to increase the chances of a gap 
+                    within a run (5 or more residues) of hydrophilic amino acids; these are likely to be loop or random coil regions where gaps are more common" />
+                <param argument="-MAXDIV" type="integer" min="0" max="100" optional="true" label="Delay divergent sequences" help="Percentage identity for delay" />
+                <param argument="-NEGATIVE" type="boolean" truevalue="-NEGATIVE" falsevalue="" checked="false" label="Negative values in matrix" help="Delays the alignment of the most distantly related sequences 
+                    until after the most closely related sequences have been aligned. The setting shows the percent identity level required to delay the addition of a sequence; sequences that are less identical 
+                    than this level to any other sequences will be aligned later" />
+                <param argument="-TRANSWEIGHT" type="float" min="0" max="1" optional="true" label="Transition weight" help="The transition weight option for aligning nucleotide sequences has been changed in version 
+                    1.7 from an on/off toggle to a weight between 0 and 1. A weight of zero means that the transitions are scored as mismatches; a weight of 1 gives transitions the full match score. For distantly 
+                    related DNA sequences, the weight should be near to zero; for closely related sequences it can be useful to assign a higher score" />
+            </section>
+        </xml>
+        <token name="@SLOW_PAIRWISE_ALIGNMENTS@"><![CDATA[
+            #if $type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPOPEN
+                -PWGAPOPEN=$type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPOPEN
+            #end if
+            #if $type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPEXT
+                -PWGAPEXT=$type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPEXT
+            #end ifx
+        ]]></token>
+        <token name="@FAST_PAIRWISE_ALIGNMENTS@"><![CDATA[
+            #if $type_conditional.algorithm_conditional.fast_pairwise_alignments.KTUPLE
+            -KTUPLE=$type_conditional.algorithm_conditional.fast_pairwise_alignments.KTUPLE
+            #end if
+            #if $type_conditional.algorithm_conditional.fast_pairwise_alignments.TOPDIAGS
+                -TOPDIAGS=$type_conditional.algorithm_conditional.fast_pairwise_alignments.TOPDIAGS
+            #end if
+            #if $type_conditional.algorithm_conditional.fast_pairwise_alignments.WINDOW
+                -WINDOW=$type_conditional.algorithm_conditional.fast_pairwise_alignments.WINDOW
+            #end if
+            #if $type_conditional.algorithm_conditional.fast_pairwise_alignments.PAIRGAP
+                -PAIRGAP=$type_conditional.algorithm_conditional.fast_pairwise_alignments.PAIRGAP
+            #end if
+            #if $type_conditional.algorithm_conditional.fast_pairwise_alignments.SCORE
+                -SCORE=$type_conditional.algorithm_conditional.fast_pairwise_alignments.SCORE
+            #end if
+        ]]></token>
+        <token name="@MULTIPLE_ALIGNMENTS@"><![CDATA[
+            #if $type_conditional.multiple_alignments.GAPOPEN
+                -GAPOPEN=$type_conditional.multiple_alignments.GAPOPEN
+            #end if
+            #if $type_conditional.multiple_alignments.GAPEXT
+                -GAPEXT=$type_conditional.multiple_alignments.GAPEXT
+            #end if
+            $type_conditional.multiple_alignments.ENDGAPS
+            #if $type_conditional.multiple_alignments.GAPDIST
+                -GAPDIST=$type_conditional.multiple_alignments.GAPDIST
+            #end if
+            $type_conditional.multiple_alignments.NOPGAP
+            $type_conditional.multiple_alignments.NOHGAP
+            #if $type_conditional.multiple_alignments.MAXDIV
+                -MAXDIV=$type_conditional.multiple_alignments.MAXDIV
+            #end if
+            $type_conditional.multiple_alignments.NEGATIVE
+            #if $type_conditional.multiple_alignments.TRANSWEIGHT
+                -TRANSWEIGHT=$type_conditional.multiple_alignments.TRANSWEIGHT
+            #end if
+        ]]></token>
+
+    </macros>
\ No newline at end of file
diff --git a/tools/clustalw/rgClustalw.xml b/tools/clustalw/rgClustalw.xml
index 465a470a2..9f1314d8c 100644
--- a/tools/clustalw/rgClustalw.xml
+++ b/tools/clustalw/rgClustalw.xml
@@ -1,11 +1,12 @@
-<tool id="clustalw" name="ClustalW" version="2.1">
+<tool id="clustalw" name="ClustalW" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <description>multiple sequence alignment program for DNA or proteins</description>
-    <requirements>
-        <requirement type="package" version="2.1">clustalw</requirement>
-    </requirements>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 ln -s '$input' input.fasta &&
-clustalw2 -INFILE=input.fasta -OUTFILE='$output' -OUTORDER=$out_order -TYPE=$dnarna
+clustalw2 -INFILE=input.fasta -OUTFILE='$output' -OUTORDER=$out_order -TYPE=$type_conditional.selector
 #if $outcontrol.outform == "clustal"
     -OUTPUT=CLUSTAL
     #if $outcontrol.out_seqnos == "ON"
@@ -21,13 +22,62 @@ clustalw2 -INFILE=input.fasta -OUTFILE='$output' -OUTORDER=$out_order -TYPE=$dna
 #if $range.mode == "part"
     -RANGE=${range.seq_range_start},${range.seq_range_end}
 #end if
+#if $type_conditional.selector == 'PROTEIN'
+    #if $type_conditional.algorithm_conditional.selector == ''
+        -PWMATRIX=$type_conditional.algorithm_conditional.slow_pairwise_alignments.PWMATRIX
+        @SLOW_PAIRWISE_ALIGNMENTS@
+    #else
+        @FAST_PAIRWISE_ALIGNMENTS@
+    #end if
+    -MATRIX=$type_conditional.multiple_alignments.MATRIX
+    @MULTIPLE_ALIGNMENTS@
+#else
+    #if $type_conditional.algorithm_conditional.selector == ''
+        -PWDNAMATRIX=$type_conditional.algorithm_conditional.slow_pairwise_alignments.PWDNAMATRIX
+        @SLOW_PAIRWISE_ALIGNMENTS@
+    #else
+        @FAST_PAIRWISE_ALIGNMENTS@
+    #end if
+    -DNAMATRIX=$type_conditional.multiple_alignments.DNAMATRIX
+    @MULTIPLE_ALIGNMENTS@
+#end if
+-OUTPUTTREE=$tree_calculation.OUTPUTTREE
+$tree_calculation.KIMURA
+$tree_calculation.TOSSGAPS
     ]]></command>
     <inputs>
         <param name="input" type="data" format="fasta" label="FASTA file" />
-        <param name="dnarna" type="select" label="Data type">
-            <option value="DNA" selected="True">DNA nucleotide sequences</option>
-            <option value="PROTEIN">Protein sequences</option>
-        </param>
+        <conditional name="type_conditional">
+            <param name="selector" type="select" label="Data type">
+                <option value="DNA" selected="True">DNA nucleotide sequences</option>
+                <option value="PROTEIN">Protein sequences</option>
+            </param>
+            <when value="DNA">
+                <expand macro="macro_options" algorithm="PWDNAMATRIX" multiple="DNAMATRIX" label="DNA" default="IUB">
+                    <option value="IUB" selected="true">IUB</option>
+                    <option value="CLUSTALW">CLUSTALW</option>
+                </expand>
+            </when>
+            <when value="PROTEIN">
+                <expand macro="macro_options" algorithm="PWMATRIX" multiple="MATRIX" label="Protein" default="GONNET">
+                    <option value="BLOSUM">BLOSUM</option>
+                    <option value="PAM">PAM</option>
+                    <option value="GONNET" selected="true">GONNET</option>
+                    <option value="ID">ID</option>
+                </expand>
+            </when>
+        </conditional>
+        <section name="tree_calculation" title="Tree calculation/BOOTSTRAP options">
+            <param argument="-OUTPUTTREE" type="select" label="Output tree/distance forma" help="Specify the output format. Default: phylip">
+                <option value="PHYLIP">PHYLIP</option>
+                <option value="DIST">DIST</option>
+                <option value="NJ">NJ</option>
+                <option value="NEXUS">NEXUS</option>
+            </param>
+            <param argument="-KIMURA" type="boolean" truevalue="-KIMURA" falsevalue="" checked="false" label="Use Kimura correction" 
+                help="For small divergence (say inferior 10%) this option makes no difference. For greater divergence, this option corrects for the fact that observed distances underestimate actual evolutionary distances." />
+            <param argument="-TOSSGAPS" type="boolean" truevalue="-TOSSGAPS" falsevalue="" checked="false" label="Ignore positions with gaps" help="Default: No" />
+        </section>
         <conditional name="outcontrol">
             <param name="outform" type="select" label="Output alignment format">
                 <option value="clustal" selected="True">Native Clustal output format</option>
@@ -69,18 +119,90 @@ clustalw2 -INFILE=input.fasta -OUTFILE='$output' -OUTORDER=$out_order -TYPE=$dna
         <test>
             <param name="input" value="rgClustal_testin.fasta" />
             <param name="outform" value="fasta" />
-            <param name="dnarna" value="DNA" />
+            <param name="dnaprotein" value="DNA" />
             <param name="mode" value="complete" />
             <param name="out_order" value="ALIGNED" />
             <output name="output" file="rgClustal_testout.fasta" ftype="fasta" />
             <output name="dnd" file="rgClustal_testin.dnd" ftype="nhx" />
         </test>
+        <!-- Test DNA options-->
+        <test expect_num_outputs="2">
+            <param name="input" value="rgClustal_testin.fasta"/>
+            <param name="out_order" value="ALIGNED"/>
+            <section name="tree_calculation">
+                <param name="OUTPUTTREE" value="PHYLIP"/>
+                <param name="KIMURA" value="true"/>
+                <param name="TOSSGAPS" value="true"/>
+            </section>
+            <conditional name="type_conditional">
+                <param name="selector" value="DNA"/>
+                <section name="multiple_alignments">
+                    <param name="DNAMATRIX" value="IUB"/>
+                    <param name="GAPOPEN" value="2"/>
+                    <param name="GAPEXT" value="1"/>
+                    <param name="ENDGAPS" value="true"/>
+                    <param name="GAPDIST" value="1"/>
+                    <param name="NOPGAP" value="true"/>
+                    <param name="NOHGAP" value="true"/>
+                    <param name="MAXDIV" value="1"/>
+                    <param name="NEGATIVE" value="true"/>
+                    <param name="TRANSWEIGHT" value="1"/>
+                </section>
+                <conditional name="algorithm_conditional">
+                    <param name="selector" value=""/>
+                    <section name="slow_pairwise_alignments">
+                        <param name="PWGAPOPEN" value="2"/>
+                        <param name="PWGAPEXT" value="1"/>
+                    </section>
+                </conditional>
+            </conditional>
+            <output name="output" file="rgClustal_testout02.aln" ftype="clustal"/>
+            <output name="dnd" file="rgClustal_testin02.dnd" ftype="nhx"/>
+        </test>
+        <!-- Test protein options and fast algorithm-->
+        <test expect_num_outputs="2">
+            <param name="input" value="rgClustal_testin_prot.fasta"/>
+            <param name="out_order" value="ALIGNED"/>
+            <section name="tree_calculation">
+                <param name="OUTPUTTREE" value="PHYLIP"/>
+                <param name="KIMURA" value="false"/>
+                <param name="TOSSGAPS" value="false"/>
+            </section>
+            <conditional name="type_conditional">
+                <param name="selector" value="PROTEIN"/>
+                <section name="multiple_alignments">
+                    <param name="MATRIX" value="BLOSUM"/>
+                    <param name="GAPOPEN" value="3"/>
+                    <param name="GAPEXT" value="1"/>
+                    <param name="ENDGAPS" value="true"/>
+                    <param name="GAPDIST" value="2"/>
+                    <param name="NOPGAP" value="true"/>
+                    <param name="NOHGAP" value="true"/>
+                    <param name="MAXDIV" value="1"/>
+                    <param name="NEGATIVE" value="true"/>
+                    <param name="TRANSWEIGHT" value="1"/>
+                </section>
+                <conditional name="algorithm_conditional">
+                    <param name="selector" value="-QUICKTREE"/>
+                    <section name="fast_pairwise_alignments">
+                        <param name="KTUPLE" value="1"/>
+                        <param name="TOPDIAGS" value="1"/>
+                        <param name="WINDOW" value="2"/>
+                        <param name="PAIRGAP" value="2"/>
+                        <param name="SCORE" value="PERCENT"/>
+                    </section>
+                </conditional>
+            </conditional>
+            <output name="output" file="rgClustal_testout03.aln" ftype="clustal"/>
+            <output name="dnd" file="rgClustal_testin03.dnd" ftype="nhx"/>
+        </test>
     </tests>
     <help><![CDATA[
-**Note**
+.. class:: infomark
 
-This tool allows you to run a multiple sequence alignment with ClustalW_ using the default options.
+**Note**
 
+This tool allows you to run a multiple sequence alignment with ClustalW_.
 You can align DNA or protein sequences in the input file which should be multiple sequences to be aligned in a FASTA file.
 
 The alignments will appear as a clustal format file or optionally, as PHYLIP or FASTA format files in your history. If you choose FASTA as
@@ -92,11 +214,13 @@ A subsequence of the alignment can be output by setting the Output complete para
 
 ----
 
+.. class:: infomark
+
 **Attribution**
 
 The first iteration of this Galaxy wrapper was written by Hans-Rudolf Hotz.
 
-It was modified by Ross Lazarus for the rgenetics project - tests and some additional parameters were added.
+It was modified by Ross Lazarus for the rgenetics project - tests and some additional parameters were added. Cristóbal Gallardo included the remaining parameters.
 
 This wrapper is released licensed under the LGPL_.
 
diff --git a/tools/clustalw/test-data/rgClustal_testin02.dnd b/tools/clustalw/test-data/rgClustal_testin02.dnd
new file mode 100644
index 000000000..b9a412cab
--- /dev/null
+++ b/tools/clustalw/test-data/rgClustal_testin02.dnd
@@ -0,0 +1,31 @@
+(
+(
+c_briggsae-chrII_+_/43862-46313:0.06106,
+c_brenneri-Cbre_Contig60_+_/627772-630087:0.05560)
+:0.01208,
+(
+c_remanei-Crem_Contig172_-_/123228-124941:0.06371,
+c_elegans-II_+_/9706834-9708803:0.06962)
+:0.01292,
+(
+(
+(
+(
+c_briggsae-chrIfooI_+_/43862-46313:0.08659,
+c_brenneri-Cbre_Contig60gak_+_/627772-630087:0.06341)
+:0.05181,
+(
+c_remanei-Crem_Contig172foo_-_/123228-124941:0.06431,
+c_elegans-II_+_more/9706834-9708803:0.05235)
+:0.03152)
+:0.04735,
+c_briggsae-chrII_+_bar/43862-46313:-0.08989)
+:0.04869,
+(
+(
+c_remanei-Crem_Contig172zot_-_/123228-124941:0.07858,
+c_elegans-II_+_meh/9706834-9708803:0.09164)
+:0.05929,
+c_brenneri-Cbre_Contig60fee_+_/627772-630087:0.12954)
+:0.03627)
+:0.07124);
diff --git a/tools/clustalw/test-data/rgClustal_testin03.dnd b/tools/clustalw/test-data/rgClustal_testin03.dnd
new file mode 100644
index 000000000..c24eb8f4b
--- /dev/null
+++ b/tools/clustalw/test-data/rgClustal_testin03.dnd
@@ -0,0 +1,103 @@
+(
+(
+(
+(
+(
+1==:0.10466,
+2==:0.11086)
+:0.03287,
+(
+3==:0.11257,
+(
+4=p:0.04128,
+5=p:0.04468)
+:0.06078)
+:0.02995)
+:0.11829,
+6==:0.25773)
+:0.01821,
+7==:0.26433)
+:0.02576,
+(
+(
+(
+8=opsin_:0.00127,
+(
+9==:0.01804,
+10==:0.02316)
+:0.00590)
+:0.08153,
+(
+11==:0.08862,
+12==:0.08818)
+:0.02496)
+:0.17382,
+13==:0.26257)
+:0.01165,
+(
+(
+(
+(
+(
+14==:0.04296,
+15==:0.04604)
+:0.10934,
+(
+16==:0.02950,
+17==:0.02077)
+:0.12646)
+:0.18931,
+(
+(
+18==:0.12161,
+19==:0.12507)
+:0.17514,
+(
+(
+(
+(
+(
+20==:0.00751,
+21==:-0.00467)
+:0.02248,
+22==:0.01604)
+:0.14593,
+(
+23==:0.04207,
+24==:0.04717)
+:0.13371)
+:0.04590,
+25==:0.22090)
+:0.02731,
+26==:0.23656)
+:0.06585)
+:0.00454)
+:0.02246,
+(
+27==:0.12163,
+28==:0.12167)
+:0.20854)
+:0.05872,
+(
+(
+29==:0.02733,
+(
+30==:0.00316,
+31=p:0.00179)
+:0.02465)
+:0.31664,
+(
+(
+32==:0.05101,
+33=p:0.05088)
+:0.26674,
+(
+(
+34==:0.00000,
+35=p:0.00000)
+:0.29806,
+36==:0.30732)
+:0.00817)
+:0.04982)
+:0.08204)
+:0.08853);
diff --git a/tools/clustalw/test-data/rgClustal_testin_prot.fasta b/tools/clustalw/test-data/rgClustal_testin_prot.fasta
new file mode 100644
index 000000000..e323c25ac
--- /dev/null
+++ b/tools/clustalw/test-data/rgClustal_testin_prot.fasta
@@ -0,0 +1,285 @@
+>     1== M63632   1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]
+MNGTEGDNFYVPFSNKTGLARSPYEYPQYYLAEPWKYSALAAYMFFLILVGFPVNFLTLF
+VTVQHKKLRTPLNYILLNLAMANLFMVLFGFTVTMYTSMNGYFVFGPTMCSIEGFFATLG
+GEVALWSLVVLAIERYIVICKPMGNFRFGNTHAIMGVAFTWIMALACAAPPLVGWSRYIP
+EGMQCSCGPDYYTLNPNFNNESYVVYMFVVHFLVPFVIIFFCYGRLLCTVKEAAAAQQES
+ASTQKAEKEVTRMVVLMVIGFLVCWVPYASVAFYIFTHQGSDFGATFMTLPAFFAKSSAL
+YNPVIYILMNKQFRNCMITTLCCGKNPLGDDESGASTSKTEVSSVSTSPVSPA
+>     2== U22180   1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]
+MNGTEGPNFYVPFSNITGVVRSPFEQPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
+VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG
+GEIGLWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP
+EGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQES
+ATTQKAEKEVTRMVIIMVIFFLICWLPYASVAMYIFTHQGSNFGPIFMTLPAFFAKTASI
+YNPIIYIMMNKQFRNCMLTSLCCGKNPLGDDEASATASKTETSQVAPA
+>     3== M92038   1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9
+MNGTEGINFYVPMSNKTGVVRSPFEYPQYYLAEPWKYRLVCCYIFFLISTGLPINLLTLL
+VTFKHKKLRQPLNYILVNLAVADLFMACFGFTVTFYTAWNGYFVFGPVGCAVEGFFATLG
+GQVALWSLVVLAIERYIVVCKPMGNFRFSATHAMMGIAFTWVMAFSCAAPPLFGWSRYMP
+EGMQCSCGPDYYTHNPDYHNESYVLYMFVIHFIIPVVVIFFSYGRLICKVREAAAQQQES
+ATTQKAEKEVTRMVILMVLGFMLAWTPYAVVAFWIFTNKGADFTATLMAVPAFFSKSSSL
+YNPIIYVLMNKQFRNCMITTICCGKNPFGDEDVSSTVSQSKTEVSSVSSSQVSPA
+>     4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish
+MNGTEGKNFYVPMSNRTGLVRSPFEYPQYYLAEPWQFKILALYLFFLMSMGLPINGLTLV
+VTAQHKKLRQPLNFILVNLAVAGTIMVCFGFTVTFYTAINGYFVLGPTGCAVEGFMATLG
+GEVALWSLVVLAIERYIVVCKPMGSFKFSSSHAFAGIAFTWVMALACAAPPLFGWSRYIP
+EGMQCSCGPDYYTLNPDYNNESYVIYMFVCHFILPVAVIFFTYGRLVCTVKAAAAQQQDS
+ASTQKAEREVTKMVILMVFGFLIAWTPYATVAAWIFFNKGADFSAKFMAIPAFFSKSSAL
+YNPVIYVLLNKQFRNCMLTTIFCGKNPLGDDESSTVSTSKTEVSSVSPA
+>     5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish
+MNGTEGNNFYVPLSNRTGLVRSPFEYPQYYLAEPWQFKLLAVYMFFLICLGLPINGLTLI
+CTAQHKKLRQPLNFILVNLAVAGAIMVCFGFTVTFYTAINGYFALGPTGCAVEGFMATLG
+GEVALWSLVVLAIERYIVVCKPMGSFKFSSTHASAGIAFTWVMAMACAAPPLVGWSRYIP
+EGIQCSCGPDYYTLNPEYNNESYVLYMFICHFILPVTIIFFTYGRLVCTVKAAAAQQQDS
+ASTQKAEREVTKMVILMVLGFLVAWTPYATVAAWIFFNKGAAFSAQFMAIPAFFSKTSAL
+YNPVIYVLLNKQFRSCMLTTLFCGKNPLGDEESSTVSTSKTEVSSVSPA
+>     6== L11864   1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-
+MKQVPEFHEDFYIPIPLDINNLSAYSPFLVPQDHLGNQGIFMAMSVFMFFIFIGGASINI
+LTILCTIQFKKLRSHLNYILVNLSIANLFVAIFGSPLSFYSFFNRYFIFGATACKIEGFL
+ATLGGMVGLWSLAVVAFERWLVICKPLGNFTFKTPHAIAGCILPWISALAASLPPLFGWS
+RYIPEGLQCSCGPDWYTTNNKYNNESYVMFLFCFCFAVPFGTIVFCYGQLLITLKLAAKA
+QADSASTQKAEREVTKMVVVMVLGFLVCWAPYASFSLWIVSHRGEEFDLRMATIPSCLSK
+ASTVYNPVIYVLMNKQFRSCMMKMVCGKNIEEDEASTSSQVTQVSSVAPEK
+>     7== M13299   1 human BCP <>[Science232(4747),193-202'86]
+MRKMSEEEFYLFKNISSVGPWDGPQYHIAPVWAFYLQAAFMGTVFLIGFPLNAMVLVATL
+RYKKLRQPLNYILVNVSFGGFLLCIFSVFPVFVASCNGYFVFGRHVCALEGFLGTVAGLV
+TGWSLAFLAFERYIVICKPFGNFRFSSKHALTVVLATWTIGIGVSIPPFFGWSRFIPEGL
+QCSCGPDWYTVGTKYRSESYTWFLFIFCFIVPLSLICFSYTQLLRALKAVAAQQQESATT
+QKAEREVSRMVVVMVGSFCVCYVPYAAFAMYMVNNRNHGLDLRLVTIPSFFSKSACIYNP
+IIYCFMNKQFQACIMKMVCGKAMTDESDTCSSQKTEVSTVSSTQVGPN
+>     8=opsin, greensensitive  human (fragment) S07060
+DLAETVIASTISIVNQVSGYFVLGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKP
+FGNVRFDAKLAIVGIAFSWIWAAVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQS
+YMIVLMVTCCITPLSIIVLCYLQVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFC
+>     9== K03494   1 human GCP <>[Science232(4747),193-202'86]
+MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM
+IFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISVVNQVYGYFV
+LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGNVRFDAKLAIVGIAFSWIWA
+AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYL
+QVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFCFCWGPYAFFACFAAANPGYPFH
+PLMAALPAFFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSS
+VSPA
+>    10== Z68193   1 human Red Opsin <>[]
+MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM
+IFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISIVNQVSGYFV
+LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGNVRFDAKLAIVGIAFSWIWS
+AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCIIPLAIIMLCYL
+QVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMIFAYCVCWGPYTFFACFAAANPGYAFH
+PLMAALPAYFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSS
+VSPA
+>    11== M92036   1 Gecko gecko P521 <retina>[PNAS89,6841-6845'92]
+MTEAWNVAVFAARRSRDDDDTTRGSVFTYTNTNNTRGPFEGPNYHIAPRWVYNLVSFFMI
+IVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVASTISVFNQIFGYFIL
+GHPLCVIEGYVVSSCGITGLWSLAIISWERWFVVCKPFGNIKFDSKLAIIGIVFSWVWAW
+GWSAPPIFGWSRYWPHGLKTSCGPDVFSGSVELGCQSFMLTLMITCCFLPLFIIIVCYLQ
+VWMAIRAVAAQQKESESTQKAEREVSRMVVVMIVAFCICWGPYASFVSFAAANPGYAFHP
+LAAALPAYFAKSATIYNPVIYVFMNRQFRNCIMQLFGKKVDDGSEASTTSRTEVSSVSNS
+SVAPA
+>    12== M62903   1 chicken visual pigment <>[BBRC173,1212-1217'90]
+MAAWEAAFAARRRHEEEDTTRDSVFTYTNSNNTRGPFEGPNYHIAPRWVYNLTSVWMIFV
+VAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIASTISVINQISGYFILGH
+PMCVVEGYTVSACGITALWSLAIISWERWFVVCKPFGNIKFDGKLAVAGILFSWLWSCAW
+TAPPIFGWSRYWPHGLKTSCGPDVFSGSSDPGVQSYMVVLMVTCCFFPLAIIILCYLQVW
+LAIRAVAAQQKESESTQKAEKEVSRMVVVMIVAYCFCWGPYTFFACFAAANPGYAFHPLA
+AALPAYFAKSATIYNPIIYVFMNRQFRNCILQLFGKKVDDGSEVSTSRTEVSSVSNSSVS
+PA
+>    13== S75720   1 chicken P-opsin <>[Science267(5203),1502-1506'95]
+MSSNSSQAPPNGTPGPFDGPQWPYQAPQSTYVGVAVLMGTVVACASVVNGLVIVVSICYK
+KLRSPLNYILVNLAVADLLVTLCGSSVSLSNNINGFFVFGRRMCELEGFMVSLTGIVGLW
+SLAILALERYVVVCKPLGDFQFQRRHAVSGCAFTWGWALLWSAPPLLGWSSYVPEGLRTS
+CGPNWYTGGSNNNSYILSLFVTCFVLPLSLILFSYTNLLLTLRAAAAQQKEADTTQRAER
+EVTRMVIVMVMAFLLCWLPYSTFALVVATHKGIIIQPVLASLPSYFSKTATVYNPIIYVF
+MNKQFQSCLLEMLCCGYQPQRTGKASPGTPGPHADVTAAGLRNKVMPAHPV
+>    14== M17718   1 D.melanogaster Rh3 <>[J.Neurosci.7,1550-1557'87]
+MESGNVSSSLFGNVSTALRPEARLSAETRLLGWNVPPEELRHIPEHWLTYPEPPESMNYL
+LGTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDFMMMVKTPIFIYNSFH
+QGYALGHLGCQIFGIIGSYTGIAAGATNAFIAYDRFNVITRPMEGKMTHGKAIAMIIFIY
+MYATPWVVACYTETWGRFVPEGYLTSCTFDYLTDNFDTRLFVACIFFFSFVCPTTMITYY
+YSQIVGHVFSHEKALRDQAKKMNVESLRSNVDKNKETAEIRIAKAAITICFLFFCSWTPY
+GVMSLIGAFGDKTLLTPGATMIPACACKMVACIDPFVYAISHPRYRMELQKRCPWLALNE
+KAPESSAVASTSTTQEPQQTTAA
+>    15== X65879   1 Drosophila pseudoobscura Dpse\Rh3 <>[Genetics132(1),193-204'92
+MEYHNVSSVLGNVSSVLRPDARLSAESRLLGWNVPPDELRHIPEHWLIYPEPPESMNYLL
+GTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDFMMMIKTPIFIYNSFHQ
+GYALGHLGCQIFGVIGSYTGIAAGATNAFIAYDRYNVITRPMEGKMTHGKAIAMIIFIYL
+YATPWVVACYTESWGRFVPEGYLTSCTFDYLTDNFDTRLFVACIFFFSFVCPTTMITYYY
+SQIVGHVFSHEKALRDQAKKMNVDSLRSNVDKSKEAAEIRIAKAAITICFLFFASWTPYG
+VMSLIGAFGDKTLLTPGATMIPACTCKMVACIDPFVYAISHPRYRMELQKRCPWLAISEK
+APESRAAISTSTTQEQQQTTAA
+>    16== M17730   1 D.melanogaster Rh4 opsin <>[J.Neurosci.7,1558-1566'87]
+MEPLCNASEPPLRPEARSSGNGDLQFLGWNVPPDQIQYIPEHWLTQLEPPASMHYMLGVF
+YIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLKAPIFNSFHRGFAIY
+LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNRNMTFTKAVIMNIIIWLYCT
+PWVVLPLTQFWDRFVPEGYLTSCSFDYLSDNFDTRLFVGTIFFFSFVCPTLMILYYYSQI
+VGHVFSHEKALREQAKKMNVESLRSNVDKSKETAEIRIAKAAITICFLFFVSWTPYGVMS
+LIGAFGDKSLLTQGATMIPACTCKLVACIDPFVYAISHPRYRLELQKRCPWLGVNEKSGE
+ISSAQSTTTQEQQQTTAA
+>    17== X65880   1 Drosophila pseudoobscura Dpse\Rh4 <>[Genetics132(1),193-204'92
+MDALCNASEPPLRPEARMSSGSDELQFLGWNVPPDQIQYIPEHWLTQLEPPASMHYMLGV
+FYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLKAPIFIYNSFHRGF
+ALGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNRNMTFTKAVIMNIIIWLYC
+TPWVVLPLTQFWDRFVPEGYLTSCSFDYLSDNFDTRLFVGTIFLFSFVVPTLMILYYYSQ
+IVGHVFNHEKALREQAKKMNVESLRSNVDKSKETAEIRIAKAAITICFLFFVSWTPYGVM
+SLIGAFGDKSLLTPGATMIPACTCKLVACIEPFVYAISHPRYRMELQKRCPWLGVNEKSG
+EASSAQSTTTQEQTQQTSAA
+>    18== D50584   1 Hemigrapsus sanguineus opsin BcRh2 <compound eye>[J.Exp.Biol.1
+MTNATGPQMAYYGAASMDFGYPEGVSIVDFVRPEIKPYVHQHWYNYPPVNPMWHYLLGVI
+YLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTNVPFFTYNCFSGGV
+WMFSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNGPKLTTGKAVVFALISWV
+IAIGCALPPFFGWGNYILEGILDSCSYDYLTQDFNTFSYNIFIFVFDYFLPAAIIVFSYV
+FIVKAIFAHEAAMRAQAKKMNVSTLRSNEADAQRAEIRIAKTALVNVSLWFICWTPYALI
+SLKGVMGDTSGITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPWFCVHETET
+KSNDDSQSNSTVAQDKA
+>    19== D50583   1 Hemigrapsus sanguineus opsin BcRh1 <compound eye>[J.Exp.Biol.1
+MANVTGPQMAFYGSGAATFGYPEGMTVADFVPDRVKHMVLDHWYNYPPVNPMWHYLLGVV
+YLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTNFPPFCYNCFSGGR
+WMFSGTYCEIYAALGAITGVCSIWTLCMISFDRYNIICNGFNGPKLTQGKATFMCGLAWV
+ISVGWSLPPFFGWGSYTLEGILDSCSYDYFTRDMNTITYNICIFIFDFFLPASVIVFSYV
+FIVKAIFAHEAAMRAQAKKMNVTNLRSNEAETQRAEIRIAKTALVNVSLWFICWTPYAAI
+TIQGLLGNAEGITPLLTTLPALLAKSCSCYNPFVYAISHPKFRLAITQHLPWFCVHEKDP
+NDVEENQSSNTQTQEKS
+>    20== K02320   1 D.melanogaster opsin <>[Cell40,851-858'85]
+MESFAVAAAQLGPHFAPLSNGSVVDKVTPDMAHLISPYWNQFPAMDPIWAKILTAYMIMI
+GMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITNTPMMGINLYFETWVLGP
+MMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGRPMTIPLALGKMYVPEGNLTSC
+GIDYLERDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKKMNVKSL
+RSSEDAEKSAEGKLAKVALVTITLWFMAWTPYLVINCMGLFKFEGLTPLNTIWGACFAKS
+AACYNPIVYGISHPKYRLALKEKCPCCVFGKVDDGKSSDAQSQATASEAESKA
+>    21== K02315   1 D.melanogaster ninaE <>[Cell40,839-850'85]
+MESFAVAAAQLGPHFAPLSNGSVVDKVTPDMAHLISPYWNQFPAMDPIWAKILTAYMIMI
+GMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITNTPMMGINLYFETWVLGP
+MMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGRPMTIPLALGKIAYIWFMSSIW
+CLAPAFGWSRYVPEGNLTSCGIDYLERDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIAA
+VSAHEKAMREQAKKMNVKSLRSSEDAEKSAEGKLAKVALVTITLWFMAWTPYLVINCMGL
+FKFEGLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVFGKVDDGKSSDA
+QSQATASEAESKA
+>    22== X65877   1 Drosophila pseudoobscura Dpse\ninaE <>[Genetics132(1),193-204'
+MDSFAAVATQLGPQFAAPSNGSVVDKVTPDMAHLISPYWDQFPAMDPIWAKILTAYMIII
+GMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITNTPMMGINLYFETWVLGP
+MMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGRPMTIPLALGKIAYIWFMSTIW
+CCLAPVFGWSRYVPEGNLTSCGIDYLERDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIA
+AVSAHEKAMREQAKKMNVKSLRSSEDADKSAEGKLAKVALVTISLWFMAWTPYLVINCMG
+LFKFEGLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVFGKVDDGKSSE
+AQSQATTSEAESKA
+>    23== M12896   1 D.melanogaster Rh2 <>[Cell44,705-710'86]
+MERSHLPETPFDLAHSGPRFQAQSSGNGSVLDNVLPDMAHLVNPYWSRFAPMDPMMSKIL
+GLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQSPVMIINFYY
+ETWVLGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGINGTPMTIKTSIMKILFI
+WMMAVFWTVMPLIGWSAYVPEGNLTACSIDYMTRMWNPRSYLITYSLFVYYTPLFLICYS
+YWFIIAAVAAHEKAMREQAKKMNVKSLRSSEDCDKSAEGKLAKVALTTISLWFMAWTPYL
+VICYFGLFKIDGLTPLTTIWGATFAKTSAVYNPIVYGISHPKYRIVLKEKCPMCVFGNTD
+EPKPDAPASDTETTSEADSKA
+>    24== X65878   1 Drosophila pseudoobscura Dpse\Rh2 <>[Genetics132(1),193-204'92
+MERSLLPEPPLAMALLGPRFEAQTGGNRSVLDNVLPDMAPLVNPHWSRFAPMDPTMSKIL
+GLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQSPVMIINFYY
+ETWVLGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGINGTPMTIKTSIMKIAFI
+WMMAVFWTIMPLIGWSSYVPEGNLTACSIDYMTRQWNPRSYLITYSLFVYYTPLFMICYS
+YWFIIATVAAHEKAMRDQAKKMNVKSLRSSEDCDKSAENKLAKVALTTISLWFMAWTPYL
+IICYFGLFKIDGLTPLTTIWGATFAKTSAVYNPIVYGISHPNDRLVLKEKCPMCVCGTTD
+EPKPDAPPSDTETTSEAESKD
+>    25== U26026   1 Apis mellifera long-wavelength rhodopsin <>[]
+MIAVSGPSYEAFSYGGQARFNNQTVVDKVPPDMLHLIDANWYQYPPLNPMWHGILGFVIG
+MLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCMSPPMVINCYYETWVL
+GPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSGKPLSINGALIRIIAIWLFSL
+GWTIAPMFGWNRYVPEGNMTACGTDYFNRGLLSASYLVCYGIWVYFVPLFLIIYSYWFII
+QAVAAHEKNMREQAKKMNVASLRSSENQNTSAECKLAKVALMTISLWFMAWTPYLVINFS
+GIFNLVKISPLFTIWGSLFAKANAVYNPIVYGISHPKYRAALFAKFPSLACAAEPSSDAV
+STTSGTTTVTDNEKSNA
+>    26== L03781   1 Limulus polyphemus opsin <>[PNAS90,6150-6154'93]
+MANQLSYSSLGWPYQPNASVVDTMPKEMLYMIHEHWYAFPPMNPLWYSILGVAMIILGII
+CVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFMMPTMTSNCFAETWILGPFMC
+EVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAAAPLTHKKATLLLLFVWIWSGGWTIL
+PFFGWSRYVPEGNLTSCTVDYLTKDWSSASYVVIYGLAVYFLPLITMIYCYFFIVHAVAE
+HEKQLREQAKKMNVASLRANADQQKQSAECRLAKVAMMTVGLWFMAWTPYLIISWAGVFS
+SGTRLTPLATIWGSVFAKANSCYNPIVYGISHPRYKAALYQRFPSLACGSGESGSDVKSE
+ASATTTMEEKPKIPEA
+>    27== X07797   1 Octopus dofleini rhodopsin <>[FEBS232(1),69-72'88]
+MVESTTLVNQTWWYNPTVDIHPHWAKFDPIPDAVYYSVGIFIGVVGIIGILGNGVVIYLF
+SKTKSLQTPANMFIINLAMSDLSFSAINGFPLKTISAFMKKWIFGKVACQLYGLLGGIFG
+FMSINTMAMISIDRYNVIGRPMAASKKMSHRRAFLMIIFVWMWSIVWSVGPVFNWGAYVP
+EGILTSCSFDYLSTDPSTRSFILCMYFCGFMLPIIIIAFCYFNIVMSVSNHEKEMAAMAK
+RLNAKELRKAQAGASAEMKLAKISMVIITQFMLSWSPYAIIALLAQFGPAEWVTPYAAEL
+PVLFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQFDEKECEDANDAEEEVVASER
+GGESRDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGYPPQGYPPQGAYPPPQGYPPQGYPP
+QGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQA
+>    28== X70498   1 Todarodes pacificus rhodopsin <retina>[FEBS317(1-2),5-11'93]
+MGRDLRDNETWWYNPSIVVHPHWREFDQVPDAVYYSLGIFIGICGIIGCGGNGIVIYLFT
+KTKSLQTPANMFIINLAFSDFTFSLVNGFPLMTISCFLKKWIFGFAACKVYGFIGGIFGF
+MSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFIMIIFVWLWSVLWAIGPIFGWGAYTLE
+GVLCNCSFDYISRDSTTRSNILCMFILGFFGPILIIFFCYFNIVMSVSNHEKEMAAMAKR
+LNAKELRKAQAGANAEMRLAKISIVIVSQFLLSWSPYAVVALLAQFGPLEWVTPYAAQLP
+VMFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQFDDKETEDDKDAETEIPAGESS
+DAAPSADAAQMKEMMAMMQKMQQQQAAYPPQGYAPPPQGYPPQGYPPQGYPPQGYPPQGY
+PPPPQGAPPQGAPPAAPPQGVDNQAYQA
+>    29== L21195   1 human serotonin 5-HT7 receptor protein <placenta and fetal bra
+MMDVNSSGRPDLYGHLRSFLLPEVGRGLPDLSPDGGADPVAGSWAPHLLSEVTASPAPTW
+DAPPDNASGCGEQINYGRVEKVVIGSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLI
+VSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAMDVMCCTASIMTLCVISIDR
+YLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGWAQNVNDDKVCLISQDFGYT
+IYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRVEPDSVIALNGIVKLQKEVE
+ECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCSC
+IPLWVERTFLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYRNINRKLSAAGMHEALK
+LAERPERPEFVLQNADYCRKKGHDS
+>    30== L15228   1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]
+MPHLLSGFLEVTASPAPTWDAPPDNVSGCGEQINYGRVEKVVIGSILTLITLLTIAGNCL
+VVISVSFVKKLRQPSNYLIVSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAM
+DVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGW
+AQNVNDDKVCLISQDFGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRV
+QPESVISLNGVVKLQKEVEECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWL
+PFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRPTSRSLLQC
+QYRNINRKLSAAGMHEALKLAERPERSEFVLQNSDHCGKKGHDT
+>    31=p A47425 serotonin receptor 5HT-7 - rat
+MPHLLSGFLEVTASPAPTWDAPPDNVSGCGEQINYGRVEKVVIGSILTLITLLTIAGNCL
+VVISVSFVKKLRQPSNYLIVSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAM
+DVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGW
+AQNVNDDKVCLISQDFGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRV
+QPESVISLNGVVKLQKEVEECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWL
+PFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRTTYRSLLQC
+QYRNINRKLSAAGMHEALKLAERPERSEFVLQNSDHCGKKGHDT
+>    32== M83181   1 human serotonin receptor <>[JBC267(11),7553-7562'92]
+MDVLSPGQGNNTTSPPAPFETGGNTTGISDVTVSYQVITSLLLGTLIFCAVLGNACVVAA
+IALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCC
+TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPED
+RSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADT
+RHGASPAPQPKKSVNGESGSRNWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGN
+SKEHLPLPSEAGPTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLP
+FFIVALVLPFCESSCHMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC
+RQ
+>    33=p A35181 serotonin receptor class 1A - rat
+MDVFSFGQGNNTTASQEPFGTGGNVTSISDVTFSYQVITSLLLGTLIFCAVLGNACVVAA
+IALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCC
+TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPED
+RSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVRKVEKKGAGT
+SLGTSSAPPPKKSLNGQPGSGDWRRCAENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGN
+SKEHLPLPSESGSNSYAPACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLP
+FFIVALVLPFCESSCHMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC
+RR
+>    34== L06803   1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]
+MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS
+HSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAV
+MLERSLHNVANYLILSLAVADLMVAVLVMPLSVVSEISKVWFLHSEVCDMWISVDVLCCT
+ASILHLVAIAMDRYWAVTSIDYIRRRSARRILLMIMVVWIVALFISIPPLFGWRDPNNDP
+DKTGTCIISQDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTE
+ETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENA
+NGVNSNSSSSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYSRTREK
+LELKRERKAARTLAIITGAFLICWLPFFIIALIGPFVDPEGIPPFARSFVLWLGYFNSLL
+NPIIYTIFSPEFRSAFQKILFGKYRRGHR
+>    35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail
+MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS
+HSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAV
+MLERSLHNVANYLILSLAVADLMVAVLVMPLSVVSEISKVWFLHSEVCDMWISVDVLCCT
+ASILHLVAIAMDRYWAVTSIDYIRRRSARRILLMIMVVWIVALFISIPPLFGWRDPNNDP
+DKTGTCIISQDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTE
+ETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENA
+NGVNSNSSSSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYSRTREK
+LELKRERKAARTLAIITGAFLICWLPFFIIALIGPFVDPEGIPPFARSFVLWLGYFNSLL
+NPIIYTIFSPEFRSAFQKILFGKYRRGHR
+>    36== X95604   1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi
+MEGAEGQEELDWEALYLRLPLQNCSWNSTGWEPNWNVTVVPNTTWWQASAPFDTPAALVR
+AAAKAVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLVMPLGAV
+YEVVQRWTLGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTNIDYIHASTAKRVGMM
+IACVWTVSFFVCIAQLLGWKDPDWNQRVSEDLRCVVSQDVGYQIFATASSFYVPVLIILI
+LYWRIYQTARKRIRRRRGATARGGVGPPPVPAGGALVAGGGSGGIAAAVVAVIGRPLPTI
+SETTTTGFTNVSSNNTSPEKQSCANGLEADPPTTGYGAVAAAYYPSLVRRKPKEAADSKR
+ERKAAKTLAIITGAFVACWLPFFVLAILVPTCDCEVSPVLTSLSLWLGYFNSTLNPVIYT
+VFSPEFRHAFQRLLCGRRVRRRRAPQ
diff --git a/tools/clustalw/test-data/rgClustal_testout02.aln b/tools/clustalw/test-data/rgClustal_testout02.aln
new file mode 100644
index 000000000..1cc4954ae
--- /dev/null
+++ b/tools/clustalw/test-data/rgClustal_testout02.aln
@@ -0,0 +1,44 @@
+CLUSTAL 2.1 multiple sequence alignment
+
+
+c_briggsae-chrIfooI_+_/43862-4      CG-CACAAAT----ATG--ATGCACA-AATCCACAA------------CC
+c_brenneri-Cbre_Contig60gak_+_      CG-CACAAAT----GTA--GTGGACA-AATCCGCAT------------CC
+c_remanei-Crem_Contig172foo_-_      -AGCACAAAT----GTA--ATGAACG-AATCCGCAT------------CC
+c_elegans-II_+_more/9706834-97      TG-CACAAAT----GTG--ATGAACG-AATCCACAT------------CC
+c_briggsae-chrII_+_bar/43862-4      ---C-CGGA-----GT----CG------ATCC-----------------C
+c_briggsae-chrII_+_/43862-4631      ----ATGAGCTTCCACA--AAA-GCATGAGCT-T-T------------CT
+c_brenneri-Cbre_Contig60_+_/62      ----ATGAGCCTCCACA--ACA-GCATGATTT-T-T------------CT
+c_remanei-Crem_Contig172_-_/12      ----ATGAGCCTCTACAAC-CG--CATGATTC-T-T------------TT
+c_elegans-II_+_/9706834-970880      ----ATGAGCCTCTAC--TACA-GCATGATTC-T-T------------CT
+c_remanei-Crem_Contig172zot_-_      ----ACGAA-----GT----CG-GT----CCC-TATAAGG---------T
+c_elegans-II_+_meh/9706834-970      ----ACGAA-----GT----CG-GT----CCC-T---GAA---------C
+c_brenneri-Cbre_Contig60fee_+_      ----ACGAA-----GT----CG-AT----CCC-TG--AAA---------T
+                                                                                      
+
+c_briggsae-chrIfooI_+_/43862-4      -TAAAGCATCTC----CGAT---AACGTTGAC---CGAA-G-T-------
+c_brenneri-Cbre_Contig60gak_+_      -CAAAGCGTCTC----CGAT---AACATTTAC---CGAA-G-T-------
+c_remanei-Crem_Contig172foo_-_      -CAACGCATCGC----CAAT---CACATTCAC----AGATG-T-------
+c_elegans-II_+_more/9706834-97      -CAATGCATCAC----CGAT---CACATTGAC----AGATG-T-------
+c_briggsae-chrII_+_bar/43862-4      -TGA-AT-------------------------------------------
+c_briggsae-chrII_+_/43862-4631      -CAG--C-TT-C----TG-C---CACATCAGCATTCAAATGATC------
+c_brenneri-Cbre_Contig60_+_/62      -CGG--C-TT-C----CG-C---CACATCCGCATTCAAATGATC------
+c_remanei-Crem_Contig172_-_/12      -CAG--C-CT-C----TG-C---CACGTCCGCATTCAAATG-CTC-----
+c_elegans-II_+_/9706834-970880      -CAG--C-TT-C----TG-C---AACGTCAGCATTCAGATGATC------
+c_remanei-Crem_Contig172zot_-_      ATGAT-T-TTATA---TGA----TGTACC-ATAAGGAAATAGT-C-----
+c_elegans-II_+_meh/9706834-970      --AAT-TATT-T----TGA----TATA---G-AAAGAAACGGTA------
+c_brenneri-Cbre_Contig60fee_+_      -CAG------ATGAG-CGGT---TG-ACC-A---GAGAACAAC-C-----
+                                                                                      
+
+c_briggsae-chrIfooI_+_/43862-4      ---------
+c_brenneri-Cbre_Contig60gak_+_      ---------
+c_remanei-Crem_Contig172foo_-_      ---------
+c_elegans-II_+_more/9706834-97      ---------
+c_briggsae-chrII_+_bar/43862-4      ---------
+c_briggsae-chrII_+_/43862-4631      ---------
+c_brenneri-Cbre_Contig60_+_/62      ---------
+c_remanei-Crem_Contig172_-_/12      ---------
+c_elegans-II_+_/9706834-970880      ---------
+c_remanei-Crem_Contig172zot_-_      ---------
+c_elegans-II_+_meh/9706834-970      ---------
+c_brenneri-Cbre_Contig60fee_+_      ---------
+                                             
diff --git a/tools/clustalw/test-data/rgClustal_testout03.aln b/tools/clustalw/test-data/rgClustal_testout03.aln
new file mode 100644
index 000000000..151e10081
--- /dev/null
+++ b/tools/clustalw/test-data/rgClustal_testout03.aln
@@ -0,0 +1,458 @@
+CLUSTAL 2.1 multiple sequence alignment
+
+
+14==            ------------------------------------MESGNV-SSSLFGNVSTA-LRPEA
+15==            ------------------------------------MEYHNV-SSVL-GNVSSV-LRPDA
+16==            ------------------------------------ME-------PL-CNASEPPLRPEA
+17==            ------------------------------------MD-------AL-CNASEPPLRPEA
+18==            -----------------------------------------------MTNATG----PQM
+19==            -----------------------------------------------MANVTG----PQM
+20==            ------------------------------------ME-SFA----VAAAQLG----PH-
+21==            ------------------------------------ME-SFA----VAAAQLG----PH-
+22==            ------------------------------------MD-SFA----AVATQLG----PQ-
+23==            ------------------------------------MERSHLPETPFDLAHSG----PR-
+24==            ------------------------------------MERSLLPEPPLAMALLG----PR-
+25==            -----------------------------------------------MIAVSG----PS-
+26==            ------------------------------------------MANQLSYSSLGW---P--
+27==            ------------------------------------------------------------
+28==            ------------------------------------------------------------
+1==             -----------------------------------------------------MNGT-E-
+2==             -----------------------------------------------------MNGT-E-
+4=p             -----------------------------------------------------MNGT-E-
+5=p             -----------------------------------------------------MNGT-E-
+3==             -----------------------------------------------------MNGT-E-
+6==             -----------------------------------------------------MKQVPEF
+7==             -----------------------------------------------------MRKMSE-
+9==             -----------------------------------------MAQQWSLQRLAGRHPQDSY
+10==            -----------------------------------------MAQQWSLQRLAGRHPQDSY
+8=opsin_        ------------------------------------------------------------
+11==            -----------------------------------------MTEAWNVAVFAARRSRDD-
+12==            -----------------------------------------MA-AWEAA-FAARRRHEE-
+13==            ------------------------------------------------------------
+30==            ------------------------------------------------------------
+31=p            ------------------------------------------------------------
+29==            ---------------------MMDVNSSGRPDLYGHLRSFLLPEVGRGLPDLSPDGGADP
+32==            -----------------------------------------------MDVL-SPGQ-GNN
+33=p            -----------------------------------------------MDVF-SFGQ-GNN
+34==            MANFTFGDLALDVARM-GGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFING
+35=p            MANFTFGDLALDVARM-GGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFING
+36==            ---------------MEGAEGQEELDWEALYLRLP-LQ---------NCSWNSTGWEPNW
+                                                                            
+
+14==            RLSA---ETRLLGWN------VPPEELRH-IPEHWLTYPE-PPES--MNYLLGT---LYI
+15==            RLSA---ESRLLGWN------VPPDELRH-IPEHWLIYPE-PPES--MNYLLGT---LYI
+16==            R-SSGNGDLQFLGWN------VPPDQIQY-IPEHWLTQLE-PPAS--MHYMLGV---FYI
+17==            RMSSGSDELQFLGWN------VPPDQIQY-IPEHWLTQLE-PPAS--MHYMLGV---FYI
+18==            AYYGAASMDFGYPEGVSIVDFVRPE-IKPYVHQHWYNY---PPVNPMWHYLLGV---IYL
+19==            AFYGSGAATFGYPEGMTVADFV-PDRVKHMVLDHWYNY---PPVNPMWHYLLGV---VYL
+20==            -F-A-PL------SNGSVVDKVTPD-MAHLISPYWNQF---PAMDPIWAKILTA---YMI
+21==            -F-A-PL------SNGSVVDKVTPD-MAHLISPYWNQF---PAMDPIWAKILTA---YMI
+22==            -F-AAP-------SNGSVVDKVTPD-MAHLISPYWDQF---PAMDPIWAKILTA---YMI
+23==            -FQAQSS------GNGSVLDNVLPD-MAHLVNPYWSRFA--P-MDPMMSKILGL---FTL
+24==            -FEAQTG------GNRSVLDNVLPD-MAPLVNPHWSRFA--P-MDPTMSKILGL---FTL
+25==            -YEAFSYGGQARFNNQTVVDKVPPD-MLHLIDANWYQY---PPLNPMWHGILG----FVI
+26==            -Y--QP--------NASVVDTMPKE-MLYMIHEHWYAF---PPMNPLWYSILGV---AMI
+27==            -----MVESTTLV-NQTW--WYNPTVDIH---PHWAKFDPIP--DAVYYS-VG----IFI
+28==            -----M--GRDLRDNETW--WYNPSIVVH---PHWREFDQVP--DAVYYS-LG----IFI
+1==             GDNFYV-PF----SNKTGLARSPYE------YPQY-YLA------EPWKYSALA---AYM
+2==             GPNFYV-PF----SNITGVVRSPFE------QPQY-YLA------EPWQFSMLA---AYM
+4=p             GKNFYV-PM----SNRTGLVRSPFE------YPQY-YLA------EPWQFKILA---LYL
+5=p             GNNFYV-PL----SNRTGLVRSPFE------YPQY-YLA------EPWQFKLLA---VYM
+3==             GINFYV-PM----SNKTGVVRSPFE------YPQY-YLA------EPWKYRLVC---CYI
+6==             HEDFYI-PIPLDINNLSAY--SPFL------VPQD-HLG------NQGIFMAMS---VFM
+7==             -EEFYLF------KNISSV--GPWD------GPQY-HIA------PVWAFYLQA---AFM
+9==             EDSTQSSIFTYTNSNST---RGPFE------GPNY-HIA------PRWVYHLTS---VWM
+10==            EDSTQSSIFTYTNSNST---RGPFE------GPNY-HIA------PRWVYHLTS---VWM
+8=opsin_        ------------------------------------------------------------
+11==            DDTTRGSVFTYTNTNNT---RGPFE------GPNY-HIA------PRWVYNLVS---FFM
+12==            EDTTRDSVFTYTNSNNT---RGPFE------GPNY-HIA------PRWVYNLTS---VWM
+13==            ----MSSNSSQAPPNGT---PGPFD------GPQWPYQA------PQSTYVGVA---VLM
+30==            -----MPHLLSGFLEVTASPAPT----WDAPPDNVSGCGEQINYGRVEKVVIGS----IL
+31=p            -----MPHLLSGFLEVTASPAPT----WDAPPDNVSGCGEQINYGRVEKVVIGS----IL
+29==            VAGSWAPHLLS---EVTASPAPT----WDAPPDNASGCGEQINYGRVEKVVIGS----IL
+32==            TTSPPAPFETGG--NTTGISDVTVS-YQ----------------------VITS---LLL
+33=p            TTASQEPFGTGG--NVTSISDVTFS-YQ----------------------VITS---LLL
+34==            SHSSRSRDNASA--NDTSATNMTDDRYW------------SLTVYSHEHLVLTS---VIL
+35=p            SHSSRSRDNASA--NDTSATNMTDDRYW------------SLTVYSHEHLVLTS---VIL
+36==            --------------NVTVVPNTT---WWQA----------SAPFDTPAALVRAAAKAVVL
+                                                                            
+
+14==            -FFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDF-MMMVK-TPIFIYNSFHQGY
+15==            -FFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDF-MMMIK-TPIFIYNSFHQGY
+16==            -FLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDL-IMCLK-APIF--NSFHRGF
+17==            -FLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDL-IMCLK-APIFIYNSFHRGF
+18==            -FLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTN-VPFFTYNCFSGG-
+19==            -FLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTN-FPPFCYNCFSGG-
+20==            -MIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLYFE--
+21==            -MIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLYFE--
+22==            -IIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLYFE--
+23==            -AIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVMIINFYYE--
+24==            -VILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVMIINFYYE--
+25==            GMLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCM-SPPMVINCYYE--
+26==            -ILGIICVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFM-MPTMTSNCFAE--
+27==            GVVGIIGILGNGVVIYLFSKTKSLQTPANMFIINLAMSDLSFSAINGFPLKTISAFMK--
+28==            GICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLVNGFPLMTISCFLK--
+1==             FFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFG-FTVTMYTSMNGY-
+2==             FLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGG-FTTTLYTSLHGY-
+4=p             FFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNLAVAGTIMVCFG-FTVTFYTAINGY-
+5=p             FFLICLGLPINGLTLICTAQHKKLRQPLNFILVNLAVAGAIMVCFG-FTVTFYTAINGY-
+3==             FFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFG-FTVTFYTAWNGY-
+6==             FFIFIGGASINILTILCTIQFKKLRSHLNYILVNLSIANLFVAIFG-SPLSFYSFFNRY-
+7==             GTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIFSVFPV-FVASCNGY-
+9==             IFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STISVVNQVYGY-
+10==            IFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STISIVNQVSGY-
+8=opsin_        --------------------------------------DLAETVIA-STISIVNQVSGY-
+11==            IIVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVA-STISVFNQIFGY-
+12==            IFVVAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIA-STISVINQISGY-
+13==            GTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLCG-SSVSLSNNINGF-
+30==            TLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDLIGG-
+31=p            TLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDLIGG-
+29==            TLITLLTIAGNCLVVISVCFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDLIGG-
+32==            GTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAALYQVLN--
+33=p            GTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAALYQVLN--
+34==            GLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVSEISK--
+35=p            GLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVSEISK--
+36==            GLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLV-MPLGAVYEVVQ--
+                                                      .         .           
+
+14==            A--LGHLGCQIFGIIGSYTGIAAGA-TNAFIAYDRFNVITRPMEG-K-MTHGKAIAMIIF
+15==            A--LGHLGCQIFGVIGSYTGIAAGA-TNAFIAYDRYNVITRPMEG-K-MTHGKAIAMIIF
+16==            AIYLGNTWCQIFASIGSYSGIGAGM-TNAAIGYDRYNVITKPMNR-N-MTFTKAVIMNII
+17==            A--LGNTWCQIFASIGSYSGIGAGM-TNAAIGYDRYNVITKPMNR-N-MTFTKAVIMNII
+18==            VWMFSPQYCEIYACLGAITGVC-SIWLLCMISFDRYNIICNGFNG-PKLTTGKAVVFALI
+19==            RWMFSGTYCEIYAALGAITGVC-SIWTLCMISFDRYNIICNGFNG-PKLTQGKATFMCGL
+20==            TWVLGPMMCDIYAGLGSAFG-CSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLALGKM--
+21==            TWVLGPMMCDIYAGLGSAFG-CSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLALGKIAY
+22==            TWVLGPMMCDIYAGLGSAFG-CSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLALGKIAY
+23==            TWVLGPLWCDIYAGCGSLFG-CVSIWSMCMIAFDRYNVIVKGING-TPMTIKTSIMKILF
+24==            TWVLGPLWCDIYAACGSLFG-CVSIWSMCMIAFDRYNVIVKGING-TPMTIKTSIMKIAF
+25==            TWVLGPLFCQIYAMLGSLFG-CGSIWTMTMIAFDRYNVIVKGLSG-KPLSINGALIRIIA
+26==            TWILGPFMCEVYGMAGSLFG-CASIWSMVMITLDRYNVIVRGMAA-APLTHKKATLLLLF
+27==            KWIFGKVACQLYGLLGGIFG-FMSINTMAMISIDRYNVIGRPMAASKKMSHRRAFLMIIF
+28==            KWIFGFAACKVYGFIGGIFG-FMSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFIMIIF
+1==             -FVFGPTMCSIEGFFATLGG-EVALWSLVVLAIERYIVICKPM-GNFRFGNTHAIMGVAF
+2==             -FVFGPTGCNLEGFFATLGG-EIGLWSLVVLAIERYVVVCKPM-SNFRFGENHAIMGVAF
+4=p             -FVLGPTGCAVEGFMATLGG-EVALWSLVVLAIERYIVVCKPM-GSFKFSSSHAFAGIAF
+5=p             -FALGPTGCAVEGFMATLGG-EVALWSLVVLAIERYIVVCKPM-GSFKFSSTHASAGIAF
+3==             -FVFGPVGCAVEGFFATLGG-QVALWSLVVLAIERYIVVCKPM-GNFRFSATHAMMGIAF
+6==             -FIFGATACKIEGFLATLGG-MVGLWSLAVVAFERWLVICKPL-GNFTFKTPHAIAGCIL
+7==             -FVFGRHVCALEGFLGTVAG-LVTGWSLAFLAFERYIVICKPF-GNFRFSSKHALTVVLA
+9==             -FVLGHPMCVLEGYTVSLCG-ITGLWSLAIISWERWMVVCKPF-GNVRFDAKLAIVGIAF
+10==            -FVLGHPMCVLEGYTVSLCG-ITGLWSLAIISWERWLVVCKPF-GNVRFDAKLAIVGIAF
+8=opsin_        -FVLGHPMCVLEGYTVSLCG-ITGLWSLAIISWERWLVVCKPF-GNVRFDAKLAIVGIAF
+11==            -FILGHPLCVIEGYVVSSCG-ITGLWSLAIISWERWFVVCKPF-GNIKFDSKLAIIGIVF
+12==            -FILGHPMCVVEGYTVSACG-ITALWSLAIISWERWFVVCKPF-GNIKFDGKLAVAGILF
+13==            -FVFGRRMCELEGFMVSLTG-IVGLWSLAILALERYVVVCKPL-GDFQFQRRHAVSGCAF
+30==            KWIFGHFFCNVFIAMDVMCC-TASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILS
+31=p            KWIFGHFFCNVFIAMDVMCC-TASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILS
+29==            KWIFGHFFCNVFIAMDVMCC-TASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILS
+32==            KWTLGQVTCDLFIALDVLCC-TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISL
+33=p            KWTLGQVTCDLFIALDVLCC-TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISL
+34==            VWFLHSEVCDMWISVDVLCC-TASILHLVAIAMDRYWAVTS-IDYIRRRSARRILLMIMV
+35=p            VWFLHSEVCDMWISVDVLCC-TASILHLVAIAMDRYWAVTS-IDYIRRRSARRILLMIMV
+36==            RWTLGPELCDMWTSGDVLCC-TASILHLVAIALDRYWAVTN-IDYIHASTAKRVGMMIAC
+                   :    * :                   :  :*:  :   :                 
+
+14==            IYMYATPWV-VACYTETW------GRFVPEGYLTSCTFDYLT--DNFDTRLFVACIFFFS
+15==            IYLYATPWV-VACYTESW------GRFVPEGYLTSCTFDYLT--DNFDTRLFVACIFFFS
+16==            IWLYCTPWV-VLPLTQFW------DRFVPEGYLTSCSFDYLS--DNFDTRLFVGTIFFFS
+17==            IWLYCTPWV-VLPLTQFW------DRFVPEGYLTSCSFDYLS--DNFDTRLFVGTIFLFS
+18==            SWVIAIGCA-LPPFF-GW------GNYILEGILDSCSYDYLT--QDFNTFSYNIFIFVFD
+19==            AWVISVGWS-LPPFF-GW------GSYTLEGILDSCSYDYFT--RDMNTITYNICIFIFD
+20==            --------------------------YVPEGNLTSCGIDYLE--RDWNPRSYLIFYSIFV
+21==            IWFMSSIWC-LAPAF-GW------SRYVPEGNLTSCGIDYLE--RDWNPRSYLIFYSIFV
+22==            IWFMSTIWCCLAPVF-GW------SRYVPEGNLTSCGIDYLE--RDWNPRSYLIFYSIFV
+23==            IWMMAVFWT-VMPLI-GW------SAYVPEGNLTACSIDYMT--RMWNPRSYLITYSLFV
+24==            IWMMAVFWT-IMPLI-GW------SSYVPEGNLTACSIDYMT--RQWNPRSYLITYSLFV
+25==            IWLFSLGWT-IAPMF-GW------NRYVPEGNMTACGTDYFN--RGLLSASYLVCYGIWV
+26==            VWIWSGGWT-ILPFF-GW------SRYVPEGNLTSCTVDYLT--KDWSSASYVVIYGLAV
+27==            VWMWSIVWS-VGPVF-NW------GAYVPEGILTSCSFDYLS--TDPSTRSFILCMYFCG
+28==            VWLWSVLWA-IGPIF-GW------GAYTLEGVLCNCSFDYIS--RDSTTRSNILCMFILG
+1==             TWIMALACA-APPLV-GW------SRYIPEGMQCSCGPDYYTLNPNFNNESYVVYMFVVH
+2==             TWVMALACA-APPLV-GW------SRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVH
+4=p             TWVMALACA-APPLF-GW------SRYIPEGMQCSCGPDYYTLNPDYNNESYVIYMFVCH
+5=p             TWVMAMACA-APPLV-GW------SRYIPEGIQCSCGPDYYTLNPEYNNESYVLYMFICH
+3==             TWVMAFSCA-APPLF-GW------SRYMPEGMQCSCGPDYYTHNPDYHNESYVLYMFVIH
+6==             PWISALAAS-LPPLF-GW------SRYIPEGLQCSCGPDWYTTNNKYNNESYVMFLFCFC
+7==             TWTIGIGVS-IPPFF-GW------SRFIPEGLQCSCGPDWYTVGTKYRSESYTWFLFIFC
+9==             SWIWAAVWT-APPIF-GW------SRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTC
+10==            SWIWSAVWT-APPIF-GW------SRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTC
+8=opsin_        SWIWAAVWT-APPIF-GW------SRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTC
+11==            SWVWAWGWS-APPIF-GW------SRYWPHGLKTSCGPDVFSGSVELGCQSFMLTLMITC
+12==            SWLWSCAWT-APPIF-GW------SRYWPHGLKTSCGPDVFSGSSDPGVQSYMVVLMVTC
+13==            TWGWALLWS-APPLL-GW------SSYVPEGLRTSCGPNWYTGGS--NNNSYILSLFVTC
+30==            VWLLSASIT-LPPLF-GW-----AQNVNDDKV---CLIS--------QDFGYTIYSTAVA
+31=p            VWLLSASIT-LPPLF-GW-----AQNVNDDKV---CLIS--------QDFGYTIYSTAVA
+29==            VWLLSASIT-LPPLF-GW-----AQNVNDDKV---CLIS--------QDFGYTIYSTAVA
+32==            TWLIGFLIS-IPPML-GWRTPE--DRSDPDA----CTIS--------KDHGYTIYSTFGA
+33=p            TWLIGFLIS-IPPML-GWRTPE--DRSDPDA----CTIS--------KDHGYTIYSTFGA
+34==            VWIVALFIS-IPPLF-GWRDPN-N---DPDKTG-TCIIS--------QDKGYTIFSTVGA
+35=p            VWIVALFIS-IPPLF-GWRDPN-N---DPDKTG-TCIIS--------QDKGYTIFSTVGA
+36==            VWTVSFFVC-IAQLL-GWKDPDWNQRVSEDL---RCVVS--------QDVGYQIFATASS
+                                             .     *  .                     
+
+14==            FVCPTTMITYYYSQIVGHVFSHEKAL----------------------------------
+15==            FVCPTTMITYYYSQIVGHVFSHEKAL----------------------------------
+16==            FVCPTLMILYYYSQIVGHVFSHEKAL----------------------------------
+17==            FVVPTLMILYYYSQIVGHVFNHEKAL----------------------------------
+18==            YFLPAAIIVFSYVFIVKAIFAHEAAM----------------------------------
+19==            FFLPASVIVFSYVFIVKAIFAHEAAM----------------------------------
+20==            YYIPLFLICYSYWFIIAAVSAHEKAM----------------------------------
+21==            YYIPLFLICYSYWFIIAAVSAHEKAM----------------------------------
+22==            YYIPLFLICYSYWFIIAAVSAHEKAM----------------------------------
+23==            YYTPLFLICYSYWFIIAAVAAHEKAM----------------------------------
+24==            YYTPLFMICYSYWFIIATVAAHEKAM----------------------------------
+25==            YFVPLFLIIYSYWFIIQAVAAHEKNM----------------------------------
+26==            YFLPLITMIYCYFFIVHAVAEHEKQL----------------------------------
+27==            FMLPIIIIAFCYFNIVMSVSNHEKEM----------------------------------
+28==            FFGPILIIFFCYFNIVMSVSNHEKEM----------------------------------
+1==             FLVPFVIIFFCYGRLLCTV-----------------------------------------
+2==             FTIPMIVIFFCYGQLVFTV-----------------------------------------
+4=p             FILPVAVIFFTYGRLVCTV-----------------------------------------
+5=p             FILPVTIIFFTYGRLVCTV-----------------------------------------
+3==             FIIPVVVIFFSYGRLICKV-----------------------------------------
+6==             FAVPFGTIVFCYGQLLITL-----------------------------------------
+7==             FIVPLSLICFSYTQLLRAL-----------------------------------------
+9==             CITPLSIIVLCYLQVWLAI-----------------------------------------
+10==            CIIPLAIIMLCYLQVWLAI-----------------------------------------
+8=opsin_        CITPLSIIVLCYLQVWLAI-----------------------------------------
+11==            CFLPLFIIIVCYLQVWMAI-----------------------------------------
+12==            CFFPLAIIILCYLQVWLAI-----------------------------------------
+13==            FVLPLSLILFSYTNLLLTL-----------------------------------------
+30==            FYIPMSVMLFMYYQIYKAARKSAAK--HKF-------------------P----------
+31=p            FYIPMSVMLFMYYQIYKAARKSAAK--HKF-------------------P----------
+29==            FYIPMSVMLFMYYQIYKAARKSAAK--HKF-------------------P----------
+32==            FYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADTRHGASP----APQPKKS----VN
+33=p            FYIPLLLMLVLYGRIFRAARFRIRKTVRKVEKKGAGTSLGTSS----APPPKKS----LN
+34==            FYLPMLVMMIIYIRIWLVARSRIRK--DKFQ--MTKARLKTEETTLVASPKTEY--SVVS
+35=p            FYLPMLVMMIIYIRIWLVARSRIRK--DKFQ--MTKARLKTEETTLVASPKTEY--SVVS
+36==            FYVPVLIILILYWRIYQTARKRIRR--RR----GATARGG------VGPPPVPAGGALVA
+                   *   :   *  :                                             
+
+14==            ----------------------------RDQAKKM----------------NVES-----
+15==            ----------------------------RDQAKKM----------------NVDS-----
+16==            ----------------------------REQAKKM----------------NVES-----
+17==            ----------------------------REQAKKM----------------NVES-----
+18==            ----------------------------RAQAKKM----------------NVST-----
+19==            ----------------------------RAQAKKM----------------NVTN-----
+20==            ----------------------------REQAKKM----------------NVKS-----
+21==            ----------------------------REQAKKM----------------NVKS-----
+22==            ----------------------------REQAKKM----------------NVKS-----
+23==            ----------------------------REQAKKM----------------NVKS-----
+24==            ----------------------------RDQAKKM----------------NVKS-----
+25==            ----------------------------REQAKKM----------------NVAS-----
+26==            ----------------------------REQAKKM----------------NVAS-----
+27==            ----------------------------AAMAKRL----------------NAKE-----
+28==            ----------------------------AAMAKRL----------------NAKE-----
+1==             ----------------------------KEAAAA--------------------------
+2==             ----------------------------KEAAAQ--------------------------
+4=p             ----------------------------KAAAAQ--------------------------
+5=p             ----------------------------KAAAAQ--------------------------
+3==             ----------------------------REAAAQ--------------------------
+6==             ----------------------------KLAAKA--------------------------
+7==             ----------------------------KAVAAQ--------------------------
+9==             ----------------------------RAVAKQ--------------------------
+10==            ----------------------------RAVAKQ--------------------------
+8=opsin_        ----------------------------RAVAKQ--------------------------
+11==            ----------------------------RAVAAQ--------------------------
+12==            ----------------------------RAVAAQ--------------------------
+13==            ----------------------------RAAAAQ--------------------------
+30==            ------------------------G-FPRVQ---------PESVISLNGVVKLQK-----
+31=p            ------------------------G-FPRVQ---------PESVISLNGVVKLQK-----
+29==            ------------------------G-FPRVE---------PDSVIALNGIVKLQK-----
+32==            GESGSRNWRLGVESKAGGALCAN-G-AVRQGDDGAALEVIE-----VHRVGNSKEHLPL-
+33=p            GQPGSGDWRRCAENRAVGTPCTN-G-AVRQGDDEATLEVIE-----VHRVGNSKEHLPL-
+34==            DCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSSSERLKQI
+35=p            DCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSSSERLKQI
+36==            ---GGGSGGIAA------AVVAVIG---RP---------LP----------TISE-----
+                                                                            
+
+14==            ---------------------LRSNV-DKNKE----------------------------
+15==            ---------------------LRSNV-DKSKE----------------------------
+16==            ---------------------LRSNV-DKSKE----------------------------
+17==            ---------------------LRSNV-DKSKE----------------------------
+18==            ---------------------LRSNEADAQR-----------------------------
+19==            ---------------------LRSNEAETQR-----------------------------
+20==            ---------------------LRSSE-DAEK-----------------------------
+21==            ---------------------LRSSE-DAEK-----------------------------
+22==            ---------------------LRSSE-DADK-----------------------------
+23==            ---------------------LRSSE-DCDK-----------------------------
+24==            ---------------------LRSSE-DCDK-----------------------------
+25==            ---------------------LRSSE-NQNT-----------------------------
+26==            ---------------------LRANA-DQQKQ----------------------------
+27==            ---------------------LRKAQ---AGA----------------------------
+28==            ---------------------LRKAQ---AGA----------------------------
+1==             ----------------------QQESASTQK-----------------------------
+2==             ----------------------QQESATTQK-----------------------------
+4=p             ----------------------QQDSASTQK-----------------------------
+5=p             ----------------------QQDSASTQK-----------------------------
+3==             ----------------------QQESATTQK-----------------------------
+6==             ----------------------QADSASTQK-----------------------------
+7==             ----------------------QQESATTQK-----------------------------
+9==             ----------------------QKESESTQK-----------------------------
+10==            ----------------------QKESESTQK-----------------------------
+8=opsin_        ----------------------QKESESTQK-----------------------------
+11==            ----------------------QKESESTQK-----------------------------
+12==            ----------------------QKESESTQK-----------------------------
+13==            ----------------------QKEADTTQR-----------------------------
+30==            ---------------------EVEECAN------------------------LSRLLKHE
+31=p            ---------------------EVEECAN------------------------LSRLLKHE
+29==            ---------------------EVEECAN------------------------LSRLLKHE
+32==            ---PSEAGPTPCA----PASFERKNERNAEA----------------------KR-----
+33=p            ---PSESGSNSYA----PACLERKNERNAEA----------------------KR-----
+34==            QIETAEAFANGCAEEASIAMLERQ-CNNGKKISSNDTP---Y---------SRTR----E
+35=p            QIETAEAFANGCAEEASIAMLERQ-CNNGKKISSNDTP---Y---------SRTR----E
+36==            --TTTTGFTNVSSNNTSP---EKQSCANGLE---ADPPTTGYGAVAAAYYPSLVRRKPKE
+                                                                            
+
+14==            -------TAEIRIAKAAITICFLFFCSWTPYGVM-SLIGAF----GDKTLLTPGATMIPA
+15==            -------AAEIRIAKAAITICFLFFASWTPYGVM-SLIGAF----GDKTLLTPGATMIPA
+16==            -------TAEIRIAKAAITICFLFFVSWTPYGVM-SLIGAF----GDKSLLTQGATMIPA
+17==            -------TAEIRIAKAAITICFLFFVSWTPYGVM-SLIGAF----GDKSLLTPGATMIPA
+18==            --------AEIRIAKTALVNVSLWFICWTPYALI-SLKGVMGDTSG----ITPLVSTLPA
+19==            --------AEIRIAKTALVNVSLWFICWTPYAAI-TIQGLLGNAEG----ITPLLTTLPA
+20==            -------SAEGKLAKVALVTITLWFMAWTPYLVINCM-GLF-KFEG----LTPLNTIWGA
+21==            -------SAEGKLAKVALVTITLWFMAWTPYLVINCM-GLF-KFEG----LTPLNTIWGA
+22==            -------SAEGKLAKVALVTISLWFMAWTPYLVINCM-GLF-KFEG----LTPLNTIWGA
+23==            -------SAEGKLAKVALTTISLWFMAWTPYLVI-CYFGLF-KIDG----LTPLTTIWGA
+24==            -------SAENKLAKVALTTISLWFMAWTPYLII-CYFGLF-KIDG----LTPLTTIWGA
+25==            -------SAECKLAKVALMTISLWFMAWTPYLVI-NFSGIF-NLVK----ISPLFTIWGS
+26==            -------SAECRLAKVAMMTVGLWFMAWTPYLII-SWAGVF-S-SGTR--LTPLATIWGS
+27==            -------SAEMKLAKISMVIITQFMLSWSPYAII-ALLAQF----GPAEWVTPYAAELPV
+28==            -------NAEMRLAKISIVIVSQFLLSWSPYAVV-ALLAQF----GPLEWVTPYAAQLPV
+1==             --------AEKEVTRMVVLMVIGFLVCWVPYASVAFYIFTH---QGSD--FGATFMTLPA
+2==             --------AEKEVTRMVIIMVIFFLICWLPYASVAMYIFTH---QGSN--FGPIFMTLPA
+4=p             --------AEREVTKMVILMVFGFLIAWTPYATVAAWIFFN---KGAD--FSAKFMAIPA
+5=p             --------AEREVTKMVILMVLGFLVAWTPYATVAAWIFFN---KGAA--FSAQFMAIPA
+3==             --------AEKEVTRMVILMVLGFMLAWTPYAVVAFWIFTN---KGAD--FTATLMAVPA
+6==             --------AEREVTKMVVVMVLGFLVCWAPYASFSLWIVSH---RGEE--FDLRMATIPS
+7==             --------AEREVSRMVVVMVGSFCVCYVPYAAFAMYMVNN---RNHG--LDLRLVTIPS
+9==             --------AEKEVTRMVVVMVLAFCFCWGPYAFFACFAAAN---PGYP--FHPLMAALPA
+10==            --------AEKEVTRMVVVMIFAYCVCWGPYTFFACFAAAN---PGYA--FHPLMAALPA
+8=opsin_        --------AEKEVTRMVVVMVLAFC-----------------------------------
+11==            --------AEREVSRMVVVMIVAFCICWGPYASFVSFAAAN---PGYA--FHPLAAALPA
+12==            --------AEKEVSRMVVVMIVAYCFCWGPYTFFACFAAAN---PGYA--FHPLAAALPA
+13==            --------AEREVTRMVIVMVMAFLLCWLPYSTFALVVATH---KGII--IQPVLASLPS
+30==            RKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFI--CGTSCSCIPLWVERTCL
+31=p            RKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFI--CGTSCSCIPLWVERTCL
+29==            RKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFI--CGTSCSCIPLWVERTFL
+32==            KMAL---ARERKTVKTLGIIMGTFILCWLPFFIVALVLPF---CESSCH-MPTLLGAIIN
+33=p            KMAL---ARERKTVKTLGIIMGTFILCWLPFFIVALVLPF---CESSCH-MPALLGAIIN
+34==            KLEL---KRERKAARTLAIITGAFLICWLPFFIIALIGPF---VD--PEGIPPFARSFVL
+35=p            KLEL---KRERKAARTLAIITGAFLICWLPFFIIALIGPF---VD--PEGIPPFARSFVL
+36==            AADS---KRERKAAKTLAIITGAFVACWLPFFVLAILVPT---CD--CE-VSPVLTSLSL
+                         * .           :                                    
+
+14==            CACKMVACIDPFVYAISHPRYRMELQKRCP--WLALNE--KAPESSAVASTSTTQEP-QQ
+15==            CTCKMVACIDPFVYAISHPRYRMELQKRCP--WLAISE--KAPESRAAISTSTTQEQ-QQ
+16==            CTCKLVACIDPFVYAISHPRYRLELQKRCP--WLGVNE--KSGEISSAQST-TTQEQ-QQ
+17==            CTCKLVACIEPFVYAISHPRYRMELQKRCP--WLGVNE--KSGEASSAQST-TTQEQTQQ
+18==            LLAKSCSCYNPFVYAISHPKYRLAITQHLP--WFCV-H--ETETKSND----DSQSN--S
+19==            LLAKSCSCYNPFVYAISHPKFRLAITQHLP--WFCV-H--EKDP--NDV--EENQSS--N
+20==            CFAKSAACYNPIVYGISHPKYRLALKEKCP---CCVFG--KVD----DGKSSDAQSQ--A
+21==            CFAKSAACYNPIVYGISHPKYRLALKEKCP---CCVFG--KVD----DGKSSDAQSQ--A
+22==            CFAKSAACYNPIVYGISHPKYRLALKEKCP---CCVFG--KVD----DGKSSEAQSQ--A
+23==            TFAKTSAVYNPIVYGISHPKYRIVLKEKCP---MCVFG--NTDEPKPDAPASDTE-----
+24==            TFAKTSAVYNPIVYGISHPNDRLVLKEKCP---MCVCG--TTDEPKPDAPPSDTE-----
+25==            LFAKANAVYNPIVYGISHPKYRAALFAKFPS-LACA------AEPSSDA-VSTTSGT--T
+26==            VFAKANSCYNPIVYGISHPRYKAALYQRFPS-LACGSG-----ESGSDV---KSEAS--A
+27==            LFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQF--DEKE-CEDANDAEEEVVASE
+28==            MFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQF--DDKE-TEDDKDAETEIPAGE
+1==             FFAKSSALYNPVIYILMNKQFRNCMITTLC----CGKNPLGDDE--SGASTSKTEVSSVS
+2==             FFAKTASIYNPIIYIMMNKQFRNCMLTSLC----CGKNPLGDDE--ASATASKTE-----
+4=p             FFSKSSALYNPVIYVLLNKQFRNCMLTTIF----CGKNPLGDDE-SSTVSTSKTEVSSVS
+5=p             FFSKTSALYNPVIYVLLNKQFRSCMLTTLF----CGKNPLGDEE-SSTVSTSKTEVSSVS
+3==             FFSKSSSLYNPIIYVLMNKQFRNCMITTIC----CGKNPFGDEDVSSTVSQSKTEVSSVS
+6==             CLSKASTVYNPVIYVLMNKQFRSCMMKMV-----CGKN-IEEDE--ASTSSQVTQVSSVA
+7==             FFSKSACIYNPIIYCFMNKQFQACIMKMV-----CGKA-MTDES--DTCSSQKTEVSTVS
+9==             FFAKSATIYNPVIYVFMNRQFRNCILQLF------G---KKVDDGSELSSASKTEVSSVS
+10==            YFAKSATIYNPVIYVFMNRQFRNCILQLF------G---KKVDDGSELSSASKTEVSSVS
+8=opsin_        ------------------------------------------------------------
+11==            YFAKSATIYNPVIYVFMNRQFRNCIMQLF------G---KKVDDGSEASTTSRTEVSSVS
+12==            YFAKSATIYNPIIYVFMNRQFRNCILQLF------G---KKVDDGSEVST-SRTEVSSVS
+13==            YFSKTATVYNPIIYVFMNKQFQSCLLEMLC----CGYQPQRTGKASPGTPGPHADVTAAG
+30==            WLGYANSLINPFIYAFFNRDLRPTSRSLLQ----CQY-RNINRKLSAAGMHEALKLAERP
+31=p            WLGYANSLINPFIYAFFNRDLRTTYRSLLQ----CQY-RNINRKLSAAGMHEALKLAERP
+29==            WLGYANSLINPFIYAFFNRDLRTTYRSLLQ----CQY-RNINRKLSAAGMHEALKLAERP
+32==            WLGYSNSLLNPVIYAYFNKDFQNAFKKIIK----CKFCRQ--------------------
+33=p            WLGYSNSLLNPVIYAYFNKDFQNAFKKIIK----CKFCRR--------------------
+34==            WLGYFNSLLNPIIYTIFSPEFRSAFQKIL-----FGKYRRGHR-----------------
+35=p            WLGYFNSLLNPIIYTIFSPEFRSAFQKIL-----FGKYRRGHR-----------------
+36==            WLGYFNSTLNPVIYTVFSPEFRHAFQRLL-----CG--RRVRRRRAPQ------------
+                                                                            
+
+14==            TTAA--------------------------------------------------------
+15==            TTAA--------------------------------------------------------
+16==            TTAA--------------------------------------------------------
+17==            TSAA--------------------------------------------------------
+18==            TVAQDKA-----------------------------------------------------
+19==            TQTQEKS-----------------------------------------------------
+20==            TASEAE-SKA--------------------------------------------------
+21==            TASEAE-SKA--------------------------------------------------
+22==            TTSEAE-SKA--------------------------------------------------
+23==            TTSEAD-SKA--------------------------------------------------
+24==            TTSEAE-SKD--------------------------------------------------
+25==            TVTDNEKSNA--------------------------------------------------
+26==            TTTMEEKPKIPEA-----------------------------------------------
+27==            R--GGESRDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGY--PPQGYPPQGAYPPPQGYPP
+28==            SSDAAPSADAAQMKEMMAMMQKMQQQQAAY----PPQGYAPPPQGYPPQG-YPP-QGYPP
+1==             T-SPVSPA----------------------------------------------------
+2==             T-SQVAPA----------------------------------------------------
+4=p             ------PA----------------------------------------------------
+5=p             ------PA----------------------------------------------------
+3==             S-SQVSPA----------------------------------------------------
+6==             ------PEK---------------------------------------------------
+7==             S-TQVGPN----------------------------------------------------
+9==             ---SVSPA----------------------------------------------------
+10==            ---SVSPA----------------------------------------------------
+8=opsin_        ------------------------------------------------------------
+11==            N-SSVAPA----------------------------------------------------
+12==            N-SSVSPA----------------------------------------------------
+13==            LRNKVMPAHPV-------------------------------------------------
+30==            ERSEFVLQNSDHCGKKGHDT----------------------------------------
+31=p            ERSEFVLQNSDHCGKKGHDT----------------------------------------
+29==            ERPEFVLQNADYCRKKGHDS----------------------------------------
+32==            ------------------------------------------------------------
+33=p            ------------------------------------------------------------
+34==            ------------------------------------------------------------
+35=p            ------------------------------------------------------------
+36==            ------------------------------------------------------------
+                                                                            
+
+14==            ----------------------------------------
+15==            ----------------------------------------
+16==            ----------------------------------------
+17==            ----------------------------------------
+18==            ----------------------------------------
+19==            ----------------------------------------
+20==            ----------------------------------------
+21==            ----------------------------------------
+22==            ----------------------------------------
+23==            ----------------------------------------
+24==            ----------------------------------------
+25==            ----------------------------------------
+26==            ----------------------------------------
+27==            QGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQA
+28==            QGYPPQGYPP---PPQGAPPQ-GAPPAAPPQGVDNQAYQA
+1==             ----------------------------------------
+2==             ----------------------------------------
+4=p             ----------------------------------------
+5=p             ----------------------------------------
+3==             ----------------------------------------
+6==             ----------------------------------------
+7==             ----------------------------------------
+9==             ----------------------------------------
+10==            ----------------------------------------
+8=opsin_        ----------------------------------------
+11==            ----------------------------------------
+12==            ----------------------------------------
+13==            ----------------------------------------
+30==            ----------------------------------------
+31=p            ----------------------------------------
+29==            ----------------------------------------
+32==            ----------------------------------------
+33=p            ----------------------------------------
+34==            ----------------------------------------
+35=p            ----------------------------------------
+36==            ----------------------------------------
+                                                        

From d97dfe394360391206f0d4f9f55a591fabd76fb9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?= <gallardoalbac@gmail.com>
Date: Thu, 15 Sep 2022 10:06:55 +0200
Subject: [PATCH 2/4] Apply suggestions from code review

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 tools/clustalw/macros.xml | 26 ++++++++++++--------------
 1 file changed, 12 insertions(+), 14 deletions(-)

diff --git a/tools/clustalw/macros.xml b/tools/clustalw/macros.xml
index 54df266b3..d9dee089a 100644
--- a/tools/clustalw/macros.xml
+++ b/tools/clustalw/macros.xml
@@ -75,48 +75,46 @@
             </section>
         </xml>
         <token name="@SLOW_PAIRWISE_ALIGNMENTS@"><![CDATA[
-            #if $type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPOPEN
+            #if str($type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPOPEN)
                 -PWGAPOPEN=$type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPOPEN
             #end if
-            #if $type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPEXT
+            #if str($type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPEXT)
                 -PWGAPEXT=$type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPEXT
             #end ifx
         ]]></token>
         <token name="@FAST_PAIRWISE_ALIGNMENTS@"><![CDATA[
-            #if $type_conditional.algorithm_conditional.fast_pairwise_alignments.KTUPLE
+            #if str($type_conditional.algorithm_conditional.fast_pairwise_alignments.KTUPLE)
             -KTUPLE=$type_conditional.algorithm_conditional.fast_pairwise_alignments.KTUPLE
             #end if
-            #if $type_conditional.algorithm_conditional.fast_pairwise_alignments.TOPDIAGS
+            #if str($type_conditional.algorithm_conditional.fast_pairwise_alignments.TOPDIAGS)
                 -TOPDIAGS=$type_conditional.algorithm_conditional.fast_pairwise_alignments.TOPDIAGS
             #end if
-            #if $type_conditional.algorithm_conditional.fast_pairwise_alignments.WINDOW
+            #if str($type_conditional.algorithm_conditional.fast_pairwise_alignments.WINDOW)
                 -WINDOW=$type_conditional.algorithm_conditional.fast_pairwise_alignments.WINDOW
             #end if
-            #if $type_conditional.algorithm_conditional.fast_pairwise_alignments.PAIRGAP
+            #if str($type_conditional.algorithm_conditional.fast_pairwise_alignments.PAIRGAP)
                 -PAIRGAP=$type_conditional.algorithm_conditional.fast_pairwise_alignments.PAIRGAP
             #end if
-            #if $type_conditional.algorithm_conditional.fast_pairwise_alignments.SCORE
-                -SCORE=$type_conditional.algorithm_conditional.fast_pairwise_alignments.SCORE
-            #end if
+            -SCORE=$type_conditional.algorithm_conditional.fast_pairwise_alignments.SCORE
         ]]></token>
         <token name="@MULTIPLE_ALIGNMENTS@"><![CDATA[
-            #if $type_conditional.multiple_alignments.GAPOPEN
+            #if str($type_conditional.multiple_alignments.GAPOPEN)
                 -GAPOPEN=$type_conditional.multiple_alignments.GAPOPEN
             #end if
-            #if $type_conditional.multiple_alignments.GAPEXT
+            #if str($type_conditional.multiple_alignments.GAPEXT)
                 -GAPEXT=$type_conditional.multiple_alignments.GAPEXT
             #end if
             $type_conditional.multiple_alignments.ENDGAPS
-            #if $type_conditional.multiple_alignments.GAPDIST
+            #if str($type_conditional.multiple_alignments.GAPDIST)
                 -GAPDIST=$type_conditional.multiple_alignments.GAPDIST
             #end if
             $type_conditional.multiple_alignments.NOPGAP
             $type_conditional.multiple_alignments.NOHGAP
-            #if $type_conditional.multiple_alignments.MAXDIV
+            #if str($type_conditional.multiple_alignments.MAXDIV)
                 -MAXDIV=$type_conditional.multiple_alignments.MAXDIV
             #end if
             $type_conditional.multiple_alignments.NEGATIVE
-            #if $type_conditional.multiple_alignments.TRANSWEIGHT
+            #if str($type_conditional.multiple_alignments.TRANSWEIGHT)
                 -TRANSWEIGHT=$type_conditional.multiple_alignments.TRANSWEIGHT
             #end if
         ]]></token>

From d7ceae66a43d4e02acf190b40b8f96cbffaa2127 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
 <gallardo@informatik.uni-freiburg.de>
Date: Thu, 15 Sep 2022 10:24:57 +0200
Subject: [PATCH 3/4] Include changes

---
 tools/clustalw/macros.xml                     | 224 +++--
 tools/clustalw/repository_dependencies.xml    |   4 -
 tools/clustalw/rgClustalw.xml                 |  16 +-
 .../clustalw/test-data/rgClustal_testin03.dnd | 103 ---
 ...l_testin02.dnd => rgClustal_testout02.dnd} |   0
 .../test-data/rgClustal_testout03.aln         | 832 +++++++++---------
 .../test-data/rgClustal_testout03.dnd         | 103 +++
 7 files changed, 616 insertions(+), 666 deletions(-)
 delete mode 100644 tools/clustalw/repository_dependencies.xml
 delete mode 100644 tools/clustalw/test-data/rgClustal_testin03.dnd
 rename tools/clustalw/test-data/{rgClustal_testin02.dnd => rgClustal_testout02.dnd} (100%)
 create mode 100644 tools/clustalw/test-data/rgClustal_testout03.dnd

diff --git a/tools/clustalw/macros.xml b/tools/clustalw/macros.xml
index d9dee089a..7adbb9801 100644
--- a/tools/clustalw/macros.xml
+++ b/tools/clustalw/macros.xml
@@ -1,122 +1,112 @@
-     <macros>
-        <token name="@TOOL_VERSION@">2.1</token>
-        <token name="@VERSION_SUFFIX@">1</token>
-        <xml name="requirements">
-            <requirements>
-                <requirement type="package" version="@TOOL_VERSION@">clustalw</requirement>
-            </requirements>
-        </xml>
-        <xml name="macro_algorithm" token_algorithm="" token_label="" token_default="">
-            <param argument="-@ALGORITHM@" type="select" label="@LABEL@ weigth matrix" help="Default: @DEFAULT@">
-                <yield/>
+    <macros>
+    <token name="@TOOL_VERSION@">2.1</token>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">clustalw</requirement>
+        </requirements>
+    </xml>
+    <xml name="macro_options" token_algorithm="" token_multiple="" token_label="" token_default="">
+        <conditional name="algorithm_conditional">
+            <param name="selector" type="select" label="Algorithm for the alignment guide tree" help="Default: slow">
+                <option value="">Slow: dynamic programming (accurate)</option>
+                <option value="-QUICKTREE">Fast: method of Wilbur and Lipman (approximate)</option>
             </param>
-        </xml>
-        <xml name="macro_multiple" token_multiple="" token_label="" token_default="">
+            <when value="">
+                <section name="slow_pairwise_alignments" title="Slow pairwise alignments options">
+                    <param argument="-@ALGORITHM@" type="select" label="@LABEL@ weigth matrix" help="Default: @DEFAULT@">
+                        <yield/>
+                    </param>
+                    <param argument="-PWGAPOPEN" type="integer" min="0" optional="true" label="Gap opening penalty" help="Default: 10" />
+                    <param argument="-PWGAPEXT" type="float" min="0" optional="true" label="Gap extension penalty" help="Default: 0.1" />
+                </section>
+            </when>
+            <when value="-QUICKTREE">
+                <section name="fast_pairwise_alignments" title="Fast pairwise alignments options">
+                    <param argument="-KTUPLE" type="integer" min="0" optional="true" label="Word size" 
+                        help="Size of exactly matching fragment that is used. Increase for speed, decrease for sensitivity. Maximum value for proteins is 2, and for DNA 4.Default: 1" />
+                    <param argument="-TOPDIAGS" type="integer" min="0" optional="true" label="Number of best diagonals" 
+                        help="Number of k-tuple matches on each diagonal. Decrease for speed; increase for sensitivity. Default: 5" />
+                    <param argument="-WINDOW" type="integer" min="0" optional="true" label="Window length"
+                        help="This is the number of diagonals around each of the best diagonals that will be used. Decrease for speed; increase for sensitivity. Default: 5" />
+                    <param argument="-PAIRGAP" type="integer" min="0" optional="true" label="Gap penalty" 
+                        help="Fast pairwise alignment gap penalty for each gap created. Default: 3" />
+                    <param argument="-SCORE" type="select" label="Score type" help="Score type to output. Default: percent">
+                        <option value="PERCENT">Percent</option>
+                        <option value="ABSOLUTE">Absolute</option>
+                    </param>
+                </section>
+            </when>
+        </conditional>
+        <section name="multiple_alignments" title="Multiple alignments options">
             <param argument="-@MULTIPLE@" type="select" label="@LABEL@ weigth matrix" help="Default: @DEFAULT@">
                 <yield/>
             </param>
-        </xml>
-       <xml name="macro_options" token_algorithm="" token_multiple="" token_label="" token_default="">
-            <conditional name="algorithm_conditional">
-                <param name="selector" type="select" label="Algorithm for the alignment guide tree" help="Default: slow">
-                    <option value="">Slow: dynamic programming (accurate)</option>
-                    <option value="-QUICKTREE">Fast: method of Wilbur and Lipman (approximate)</option>
-                </param>
-                <when value="">
-                    <section name="slow_pairwise_alignments" title="Slow pairwise alignments options">
-                        <expand macro="macro_algorithm" algorithm="@ALGORITHM@" label="@LABEL@" default="@DEFAULT@">
-                            <yield/>
-                        </expand>
-                        <param argument="-PWGAPOPEN" type="integer" min="0" optional="true" label="Gap opening penalty" help="Default: 10" />
-                        <param argument="-PWGAPEXT" type="float" min="0" optional="true" label="Gap extension penalty" help="Default: 0.1" />
-                    </section>
-                </when>
-                <when value="-QUICKTREE">
-                    <section name="fast_pairwise_alignments" title="Fast pairwise alignments options">
-                        <param argument="-KTUPLE" type="integer" min="0" optional="true" label="Word size" 
-                            help="Size of exactly matching fragment that is used. Increase for speed, decrease for sensitivity. Maximum value for proteins is 2, and for DNA 4.Default: 1" />
-                        <param argument="-TOPDIAGS" type="integer" min="0" optional="true" label="Number of best diagonals" 
-                            help="Number of k-tuple matches on each diagonal. Decrease for speed; increase for sensitivity. Default: 5" />
-                        <param argument="-WINDOW" type="integer" min="0" optional="true" label="Window length"
-                            help="This is the number of diagonals around each of the best diagonals that will be used. Decrease for speed; increase for sensitivity. Default: 5" />
-                        <param argument="-PAIRGAP" type="integer" min="0" optional="true" label="Gap penalty" 
-                            help="Fast pairwise alignment gap penalty for each gap created. Default: 3" />
-                        <param argument="-SCORE" type="select" label="Score type" help="Score type to output. Default: percent">
-                            <option value="PERCENT">Percent</option>
-                            <option value="ABSOLUTE">Absolute</option>
-                        </param>
-                    </section>
-                </when>
-            </conditional>
-            <section name="multiple_alignments" title="Multiple alignments options">
-                <expand macro="macro_multiple" multiple="@MULTIPLE@" label="@LABEL@" default="@DEFAULT@">
-                    <yield/>
-                </expand>
-                <param argument="-GAPOPEN" type="integer" min="0" optional="true" label="Gap opening penalty" help="Default: 10" />
-                <param argument="-GAPEXT" type="float" min="0" optional="true" label="Gap extension penalty" help="Default: 0.2" />
-                <param argument="-ENDGAPS" type="boolean" truevalue="-ENDGAPS" falsevalue="" checked="false" label="End gap separation penalty" 
-                    help="End gap separation treats end gaps just like internal gaps for the purposes of avoiding gaps that are too close. If you turn this off, end gaps will be ignored for this purpose. 
-                        This is useful when you wish to align fragments where the end gaps are not biologically meaningful" />
-                <param argument="-GAPDIST" type="integer" min="0" optional="true" label="Gap separation penalty range" 
-                    help="Gap separation distance tries to decrease the chances of gaps being too close to each other. Gaps that are less than this distance apart are penalised more than other gaps. 
-                        This does not prevent close gaps; it makes them less frequent, promoting a block-like appearance of the alignment" />
-                <param argument="-NOPGAP" type="boolean" truevalue="-NOPGAP" falsevalue="" checked="false" label="Residue specific penalties" 
-                    help="Residue specific penalties are amino acid specific gap penalties that reduce or increase the gap opening penalties at each position in the alignment or sequence. As an example, 
-                        positions that are rich in glycine are more likely to have an adjacent gap than positions that are rich in valine" />
-                <param argument="-NOHGAP" type="boolean" truevalue="-NOHGAP" falsevalue="" checked="false" label="Hydrophilic gaps" help="Hydrophilic gap penalties are used to increase the chances of a gap 
-                    within a run (5 or more residues) of hydrophilic amino acids; these are likely to be loop or random coil regions where gaps are more common" />
-                <param argument="-MAXDIV" type="integer" min="0" max="100" optional="true" label="Delay divergent sequences" help="Percentage identity for delay" />
-                <param argument="-NEGATIVE" type="boolean" truevalue="-NEGATIVE" falsevalue="" checked="false" label="Negative values in matrix" help="Delays the alignment of the most distantly related sequences 
-                    until after the most closely related sequences have been aligned. The setting shows the percent identity level required to delay the addition of a sequence; sequences that are less identical 
-                    than this level to any other sequences will be aligned later" />
-                <param argument="-TRANSWEIGHT" type="float" min="0" max="1" optional="true" label="Transition weight" help="The transition weight option for aligning nucleotide sequences has been changed in version 
-                    1.7 from an on/off toggle to a weight between 0 and 1. A weight of zero means that the transitions are scored as mismatches; a weight of 1 gives transitions the full match score. For distantly 
-                    related DNA sequences, the weight should be near to zero; for closely related sequences it can be useful to assign a higher score" />
-            </section>
-        </xml>
-        <token name="@SLOW_PAIRWISE_ALIGNMENTS@"><![CDATA[
-            #if str($type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPOPEN)
-                -PWGAPOPEN=$type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPOPEN
-            #end if
-            #if str($type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPEXT)
-                -PWGAPEXT=$type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPEXT
-            #end ifx
-        ]]></token>
-        <token name="@FAST_PAIRWISE_ALIGNMENTS@"><![CDATA[
-            #if str($type_conditional.algorithm_conditional.fast_pairwise_alignments.KTUPLE)
-            -KTUPLE=$type_conditional.algorithm_conditional.fast_pairwise_alignments.KTUPLE
-            #end if
-            #if str($type_conditional.algorithm_conditional.fast_pairwise_alignments.TOPDIAGS)
-                -TOPDIAGS=$type_conditional.algorithm_conditional.fast_pairwise_alignments.TOPDIAGS
-            #end if
-            #if str($type_conditional.algorithm_conditional.fast_pairwise_alignments.WINDOW)
-                -WINDOW=$type_conditional.algorithm_conditional.fast_pairwise_alignments.WINDOW
-            #end if
-            #if str($type_conditional.algorithm_conditional.fast_pairwise_alignments.PAIRGAP)
-                -PAIRGAP=$type_conditional.algorithm_conditional.fast_pairwise_alignments.PAIRGAP
-            #end if
-            -SCORE=$type_conditional.algorithm_conditional.fast_pairwise_alignments.SCORE
-        ]]></token>
-        <token name="@MULTIPLE_ALIGNMENTS@"><![CDATA[
-            #if str($type_conditional.multiple_alignments.GAPOPEN)
-                -GAPOPEN=$type_conditional.multiple_alignments.GAPOPEN
-            #end if
-            #if str($type_conditional.multiple_alignments.GAPEXT)
-                -GAPEXT=$type_conditional.multiple_alignments.GAPEXT
-            #end if
-            $type_conditional.multiple_alignments.ENDGAPS
-            #if str($type_conditional.multiple_alignments.GAPDIST)
-                -GAPDIST=$type_conditional.multiple_alignments.GAPDIST
-            #end if
-            $type_conditional.multiple_alignments.NOPGAP
-            $type_conditional.multiple_alignments.NOHGAP
-            #if str($type_conditional.multiple_alignments.MAXDIV)
-                -MAXDIV=$type_conditional.multiple_alignments.MAXDIV
-            #end if
-            $type_conditional.multiple_alignments.NEGATIVE
-            #if str($type_conditional.multiple_alignments.TRANSWEIGHT)
-                -TRANSWEIGHT=$type_conditional.multiple_alignments.TRANSWEIGHT
-            #end if
-        ]]></token>
+            <param argument="-GAPOPEN" type="integer" min="0" optional="true" label="Gap opening penalty" help="Default: 10" />
+            <param argument="-GAPEXT" type="float" min="0" optional="true" label="Gap extension penalty" help="Default: 0.2" />
+            <param argument="-ENDGAPS" type="boolean" truevalue="-ENDGAPS" falsevalue="" checked="false" label="End gap separation penalty" 
+                help="End gap separation treats end gaps just like internal gaps for the purposes of avoiding gaps that are too close. If you turn this off, end gaps will be ignored for this purpose. 
+                    This is useful when you wish to align fragments where the end gaps are not biologically meaningful" />
+            <param argument="-GAPDIST" type="integer" min="0" optional="true" label="Gap separation penalty range" 
+                help="Gap separation distance tries to decrease the chances of gaps being too close to each other. Gaps that are less than this distance apart are penalised more than other gaps. 
+                    This does not prevent close gaps; it makes them less frequent, promoting a block-like appearance of the alignment" />
+            <param argument="-NOPGAP" type="boolean" truevalue="-NOPGAP" falsevalue="" checked="false" label="Residue specific penalties" 
+                help="Residue specific penalties are amino acid specific gap penalties that reduce or increase the gap opening penalties at each position in the alignment or sequence. As an example, 
+                    positions that are rich in glycine are more likely to have an adjacent gap than positions that are rich in valine" />
+            <param argument="-NOHGAP" type="boolean" truevalue="-NOHGAP" falsevalue="" checked="false" label="Hydrophilic gaps" help="Hydrophilic gap penalties are used to increase the chances of a gap 
+                within a run (5 or more residues) of hydrophilic amino acids; these are likely to be loop or random coil regions where gaps are more common" />
+            <param argument="-MAXDIV" type="integer" min="0" max="100" optional="true" label="Delay divergent sequences" help="Percentage identity for delay" />
+            <param argument="-NEGATIVE" type="boolean" truevalue="-NEGATIVE" falsevalue="" checked="false" label="Negative values in matrix" help="Delays the alignment of the most distantly related sequences 
+                until after the most closely related sequences have been aligned. The setting shows the percent identity level required to delay the addition of a sequence; sequences that are less identical 
+                than this level to any other sequences will be aligned later" />
+            <param argument="-TRANSWEIGHT" type="float" min="0" max="1" optional="true" label="Transition weight" help="The transition weight option for aligning nucleotide sequences has been changed in version 
+                1.7 from an on/off toggle to a weight between 0 and 1. A weight of zero means that the transitions are scored as mismatches; a weight of 1 gives transitions the full match score. For distantly 
+                related DNA sequences, the weight should be near to zero; for closely related sequences it can be useful to assign a higher score" />
+        </section>
+    </xml>
+    <token name="@SLOW_PAIRWISE_ALIGNMENTS@"><![CDATA[
+        #if str($type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPOPEN)
+            -PWGAPOPEN=$type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPOPEN
+        #end if
+        #if str($type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPEXT)
+            -PWGAPEXT=$type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPEXT
+        #end ifx
+    ]]></token>
+    <token name="@FAST_PAIRWISE_ALIGNMENTS@"><![CDATA[
+        #if str($type_conditional.algorithm_conditional.fast_pairwise_alignments.KTUPLE)
+        -KTUPLE=$type_conditional.algorithm_conditional.fast_pairwise_alignments.KTUPLE
+        #end if
+        #if str($type_conditional.algorithm_conditional.fast_pairwise_alignments.TOPDIAGS)
+            -TOPDIAGS=$type_conditional.algorithm_conditional.fast_pairwise_alignments.TOPDIAGS
+        #end if
+        #if str($type_conditional.algorithm_conditional.fast_pairwise_alignments.WINDOW)
+            -WINDOW=$type_conditional.algorithm_conditional.fast_pairwise_alignments.WINDOW
+        #end if
+        #if str($type_conditional.algorithm_conditional.fast_pairwise_alignments.PAIRGAP)
+            -PAIRGAP=$type_conditional.algorithm_conditional.fast_pairwise_alignments.PAIRGAP
+        #end if
+        -SCORE=$type_conditional.algorithm_conditional.fast_pairwise_alignments.SCORE
+    ]]></token>
+    <token name="@MULTIPLE_ALIGNMENTS@"><![CDATA[
+        #if str($type_conditional.multiple_alignments.GAPOPEN)
+            -GAPOPEN=$type_conditional.multiple_alignments.GAPOPEN
+        #end if
+        #if str($type_conditional.multiple_alignments.GAPEXT)
+            -GAPEXT=$type_conditional.multiple_alignments.GAPEXT
+        #end if
+        $type_conditional.multiple_alignments.ENDGAPS
+        #if str($type_conditional.multiple_alignments.GAPDIST)
+            -GAPDIST=$type_conditional.multiple_alignments.GAPDIST
+        #end if
+        $type_conditional.multiple_alignments.NOPGAP
+        $type_conditional.multiple_alignments.NOHGAP
+        #if str($type_conditional.multiple_alignments.MAXDIV)
+            -MAXDIV=$type_conditional.multiple_alignments.MAXDIV
+        #end if
+        $type_conditional.multiple_alignments.NEGATIVE
+        #if str($type_conditional.multiple_alignments.TRANSWEIGHT)
+            -TRANSWEIGHT=$type_conditional.multiple_alignments.TRANSWEIGHT
+        #end if
+    ]]></token>
 
-    </macros>
\ No newline at end of file
+</macros>
\ No newline at end of file
diff --git a/tools/clustalw/repository_dependencies.xml b/tools/clustalw/repository_dependencies.xml
deleted file mode 100644
index 2dbf5f24b..000000000
--- a/tools/clustalw/repository_dependencies.xml
+++ /dev/null
@@ -1,4 +0,0 @@
-<?xml version="1.0"?>
-<repositories>
-    <repository name="emboss_datatypes" owner="devteam" />
-</repositories>
diff --git a/tools/clustalw/rgClustalw.xml b/tools/clustalw/rgClustalw.xml
index 9f1314d8c..67b49914a 100644
--- a/tools/clustalw/rgClustalw.xml
+++ b/tools/clustalw/rgClustalw.xml
@@ -6,7 +6,7 @@
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 ln -s '$input' input.fasta &&
-clustalw2 -INFILE=input.fasta -OUTFILE='$output' -OUTORDER=$out_order -TYPE=$type_conditional.selector
+clustalw2 -INFILE=input.fasta -OUTFILE='$output' -OUTORDER=$out_order -TYPE=$type_conditional.dnarna
 #if $outcontrol.outform == "clustal"
     -OUTPUT=CLUSTAL
     #if $outcontrol.out_seqnos == "ON"
@@ -22,7 +22,7 @@ clustalw2 -INFILE=input.fasta -OUTFILE='$output' -OUTORDER=$out_order -TYPE=$typ
 #if $range.mode == "part"
     -RANGE=${range.seq_range_start},${range.seq_range_end}
 #end if
-#if $type_conditional.selector == 'PROTEIN'
+#if $type_conditional.dnarna == 'PROTEIN'
     #if $type_conditional.algorithm_conditional.selector == ''
         -PWMATRIX=$type_conditional.algorithm_conditional.slow_pairwise_alignments.PWMATRIX
         @SLOW_PAIRWISE_ALIGNMENTS@
@@ -48,7 +48,7 @@ $tree_calculation.TOSSGAPS
     <inputs>
         <param name="input" type="data" format="fasta" label="FASTA file" />
         <conditional name="type_conditional">
-            <param name="selector" type="select" label="Data type">
+            <param name="dnarna" type="select" label="Data type">
                 <option value="DNA" selected="True">DNA nucleotide sequences</option>
                 <option value="PROTEIN">Protein sequences</option>
             </param>
@@ -119,7 +119,9 @@ $tree_calculation.TOSSGAPS
         <test>
             <param name="input" value="rgClustal_testin.fasta" />
             <param name="outform" value="fasta" />
-            <param name="dnaprotein" value="DNA" />
+            <conditional name="type_conditional">
+                <param name="dnarna" value="DNA"/>
+            </conditional>
             <param name="mode" value="complete" />
             <param name="out_order" value="ALIGNED" />
             <output name="output" file="rgClustal_testout.fasta" ftype="fasta" />
@@ -135,7 +137,7 @@ $tree_calculation.TOSSGAPS
                 <param name="TOSSGAPS" value="true"/>
             </section>
             <conditional name="type_conditional">
-                <param name="selector" value="DNA"/>
+                <param name="dnarna" value="DNA"/>
                 <section name="multiple_alignments">
                     <param name="DNAMATRIX" value="IUB"/>
                     <param name="GAPOPEN" value="2"/>
@@ -157,7 +159,7 @@ $tree_calculation.TOSSGAPS
                 </conditional>
             </conditional>
             <output name="output" file="rgClustal_testout02.aln" ftype="clustal"/>
-            <output name="dnd" file="rgClustal_testin02.dnd" ftype="nhx"/>
+            <output name="dnd" file="rgClustal_testout02.dnd" ftype="nhx"/>
         </test>
         <!-- Test protein options and fast algorithm-->
         <test expect_num_outputs="2">
@@ -194,7 +196,7 @@ $tree_calculation.TOSSGAPS
                 </conditional>
             </conditional>
             <output name="output" file="rgClustal_testout03.aln" ftype="clustal"/>
-            <output name="dnd" file="rgClustal_testin03.dnd" ftype="nhx"/>
+            <output name="dnd" file="rgClustal_testout03.dnd" ftype="nhx"/>
         </test>
     </tests>
     <help><![CDATA[
diff --git a/tools/clustalw/test-data/rgClustal_testin03.dnd b/tools/clustalw/test-data/rgClustal_testin03.dnd
deleted file mode 100644
index c24eb8f4b..000000000
--- a/tools/clustalw/test-data/rgClustal_testin03.dnd
+++ /dev/null
@@ -1,103 +0,0 @@
-(
-(
-(
-(
-(
-1==:0.10466,
-2==:0.11086)
-:0.03287,
-(
-3==:0.11257,
-(
-4=p:0.04128,
-5=p:0.04468)
-:0.06078)
-:0.02995)
-:0.11829,
-6==:0.25773)
-:0.01821,
-7==:0.26433)
-:0.02576,
-(
-(
-(
-8=opsin_:0.00127,
-(
-9==:0.01804,
-10==:0.02316)
-:0.00590)
-:0.08153,
-(
-11==:0.08862,
-12==:0.08818)
-:0.02496)
-:0.17382,
-13==:0.26257)
-:0.01165,
-(
-(
-(
-(
-(
-14==:0.04296,
-15==:0.04604)
-:0.10934,
-(
-16==:0.02950,
-17==:0.02077)
-:0.12646)
-:0.18931,
-(
-(
-18==:0.12161,
-19==:0.12507)
-:0.17514,
-(
-(
-(
-(
-(
-20==:0.00751,
-21==:-0.00467)
-:0.02248,
-22==:0.01604)
-:0.14593,
-(
-23==:0.04207,
-24==:0.04717)
-:0.13371)
-:0.04590,
-25==:0.22090)
-:0.02731,
-26==:0.23656)
-:0.06585)
-:0.00454)
-:0.02246,
-(
-27==:0.12163,
-28==:0.12167)
-:0.20854)
-:0.05872,
-(
-(
-29==:0.02733,
-(
-30==:0.00316,
-31=p:0.00179)
-:0.02465)
-:0.31664,
-(
-(
-32==:0.05101,
-33=p:0.05088)
-:0.26674,
-(
-(
-34==:0.00000,
-35=p:0.00000)
-:0.29806,
-36==:0.30732)
-:0.00817)
-:0.04982)
-:0.08204)
-:0.08853);
diff --git a/tools/clustalw/test-data/rgClustal_testin02.dnd b/tools/clustalw/test-data/rgClustal_testout02.dnd
similarity index 100%
rename from tools/clustalw/test-data/rgClustal_testin02.dnd
rename to tools/clustalw/test-data/rgClustal_testout02.dnd
diff --git a/tools/clustalw/test-data/rgClustal_testout03.aln b/tools/clustalw/test-data/rgClustal_testout03.aln
index 151e10081..e238ca487 100644
--- a/tools/clustalw/test-data/rgClustal_testout03.aln
+++ b/tools/clustalw/test-data/rgClustal_testout03.aln
@@ -1,458 +1,420 @@
 CLUSTAL 2.1 multiple sequence alignment
 
 
-14==            ------------------------------------MESGNV-SSSLFGNVSTA-LRPEA
-15==            ------------------------------------MEYHNV-SSVL-GNVSSV-LRPDA
-16==            ------------------------------------ME-------PL-CNASEPPLRPEA
-17==            ------------------------------------MD-------AL-CNASEPPLRPEA
-18==            -----------------------------------------------MTNATG----PQM
-19==            -----------------------------------------------MANVTG----PQM
-20==            ------------------------------------ME-SFA----VAAAQLG----PH-
-21==            ------------------------------------ME-SFA----VAAAQLG----PH-
-22==            ------------------------------------MD-SFA----AVATQLG----PQ-
-23==            ------------------------------------MERSHLPETPFDLAHSG----PR-
-24==            ------------------------------------MERSLLPEPPLAMALLG----PR-
-25==            -----------------------------------------------MIAVSG----PS-
-26==            ------------------------------------------MANQLSYSSLGW---P--
-27==            ------------------------------------------------------------
-28==            ------------------------------------------------------------
-1==             -----------------------------------------------------MNGT-E-
-2==             -----------------------------------------------------MNGT-E-
-4=p             -----------------------------------------------------MNGT-E-
-5=p             -----------------------------------------------------MNGT-E-
-3==             -----------------------------------------------------MNGT-E-
-6==             -----------------------------------------------------MKQVPEF
-7==             -----------------------------------------------------MRKMSE-
-9==             -----------------------------------------MAQQWSLQRLAGRHPQDSY
-10==            -----------------------------------------MAQQWSLQRLAGRHPQDSY
+14==            -------------------------------------MESGNVS-SSLFGN-VSTALRPE
+15==            -----------------------------------MEYHNVSSVLGN--VS-SVLRPD--
+16==            ----------------------------------MEPLCNASEPPLRPEAR-SS------
+17==            ----------------------------------MDALCNASEPPLRPEAR-MS------
+18==            ----------------------------------------MTN-ATGPQMAYYG-AASMD
+19==            ---------------------------------------MANV--TGPQMAFYGSGA-AT
+20==            ---------------------------MESFA------VAAAQLGPHF-AP-LSN-GS--
+21==            ---------------------------MESFA------VAAAQLGPHF-AP-LSN-GS--
+22==            ---------------------------MDSFA------AVATQLGPQF-AA-PSN-GS--
+23==            ---------------------------MERSHLPETPFDLAHS-GPRFQAQ-SSG-NG--
+24==            ---------------------------MERSLLPEPPLAMALL-GPRFEAQ-TGG-NR--
+25==            --------------------------------------MIAVS-GPSYEAFSYGGQARF-
+26==            ---------------------------------------MANQLSYSSLGWPYQPNAS--
+27==            ----------------------------------------------------MVE-----
+28==            ----------------------------------------------------MG------
+9==             ---------------------------------------MAQQWSLQRLAGRHPQDSYE-
+10==            ---------------------------------------MAQQWSLQRLAGRHPQDSYE-
 8=opsin_        ------------------------------------------------------------
-11==            -----------------------------------------MTEAWNVAVFAARRSRDD-
-12==            -----------------------------------------MA-AWEAA-FAARRRHEE-
-13==            ------------------------------------------------------------
-30==            ------------------------------------------------------------
-31=p            ------------------------------------------------------------
-29==            ---------------------MMDVNSSGRPDLYGHLRSFLLPEVGRGLPDLSPDGGADP
-32==            -----------------------------------------------MDVL-SPGQ-GNN
-33=p            -----------------------------------------------MDVF-SFGQ-GNN
-34==            MANFTFGDLALDVARM-GGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFING
-35=p            MANFTFGDLALDVARM-GGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFING
-36==            ---------------MEGAEGQEELDWEALYLRLP-LQ---------NCSWNSTGWEPNW
+11==            -----------------------------------MTEAWNV-A---VFAARR--SRDD-
+12==            --------------------------------------MAAWEA---AFAARR--RHEE-
+1==             ----------------------------------------MN--G---TEGDNFYVPFS-
+2==             ----------------------------------------MN--G---TEGPNFYVPFS-
+4=p             ----------------------------------------MN--G---TEGKNFYVPMS-
+5=p             ----------------------------------------MN--G---TEGNNFYVPLS-
+3==             ----------------------------------------MN--G---TEGINFYVPMS-
+6==             ----------------------------------------MKQ-VPEFHEDFYIPIPLD-
+7==             ---------------------------------------MRKM-S---EEEFYLFKNIS-
+13==            ----------------------------------------MS--S-------NSSQAPP-
+30==            --------------------------------------------MPHLLS-GFLE-----
+31=p            --------------------------------------------MPHLLS-GFLE-----
+29==            -------MMDVNSSGRPDLYGHLRSFLLPEVGRGLPDLSPDGGADPVAGSWAPHLLSE--
+32==            -------------------------------------------------MDVL-------
+33=p            -------------------------------------------------MDVF-------
+34==            MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGL---VTSDFNDSYGLTGQFI
+35=p            MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGL---VTSDFNDSYGLTGQFI
+36==            --------------------ME-GAEGQEELDWEALYL-RLPLQNCSWNSTGWEPN----
                                                                             
 
-14==            RLSA---ETRLLGWN------VPPEELRH-IPEHWLTYPE-PPES--MNYLLGT---LYI
-15==            RLSA---ESRLLGWN------VPPDELRH-IPEHWLIYPE-PPES--MNYLLGT---LYI
-16==            R-SSGNGDLQFLGWN------VPPDQIQY-IPEHWLTQLE-PPAS--MHYMLGV---FYI
-17==            RMSSGSDELQFLGWN------VPPDQIQY-IPEHWLTQLE-PPAS--MHYMLGV---FYI
-18==            AYYGAASMDFGYPEGVSIVDFVRPE-IKPYVHQHWYNY---PPVNPMWHYLLGV---IYL
-19==            AFYGSGAATFGYPEGMTVADFV-PDRVKHMVLDHWYNY---PPVNPMWHYLLGV---VYL
-20==            -F-A-PL------SNGSVVDKVTPD-MAHLISPYWNQF---PAMDPIWAKILTA---YMI
-21==            -F-A-PL------SNGSVVDKVTPD-MAHLISPYWNQF---PAMDPIWAKILTA---YMI
-22==            -F-AAP-------SNGSVVDKVTPD-MAHLISPYWDQF---PAMDPIWAKILTA---YMI
-23==            -FQAQSS------GNGSVLDNVLPD-MAHLVNPYWSRFA--P-MDPMMSKILGL---FTL
-24==            -FEAQTG------GNRSVLDNVLPD-MAPLVNPHWSRFA--P-MDPTMSKILGL---FTL
-25==            -YEAFSYGGQARFNNQTVVDKVPPD-MLHLIDANWYQY---PPLNPMWHGILG----FVI
-26==            -Y--QP--------NASVVDTMPKE-MLYMIHEHWYAF---PPMNPLWYSILGV---AMI
-27==            -----MVESTTLV-NQTW--WYNPTVDIH---PHWAKFDPIP--DAVYYS-VG----IFI
-28==            -----M--GRDLRDNETW--WYNPSIVVH---PHWREFDQVP--DAVYYS-LG----IFI
-1==             GDNFYV-PF----SNKTGLARSPYE------YPQY-YLA------EPWKYSALA---AYM
-2==             GPNFYV-PF----SNITGVVRSPFE------QPQY-YLA------EPWQFSMLA---AYM
-4=p             GKNFYV-PM----SNRTGLVRSPFE------YPQY-YLA------EPWQFKILA---LYL
-5=p             GNNFYV-PL----SNRTGLVRSPFE------YPQY-YLA------EPWQFKLLA---VYM
-3==             GINFYV-PM----SNKTGVVRSPFE------YPQY-YLA------EPWKYRLVC---CYI
-6==             HEDFYI-PIPLDINNLSAY--SPFL------VPQD-HLG------NQGIFMAMS---VFM
-7==             -EEFYLF------KNISSV--GPWD------GPQY-HIA------PVWAFYLQA---AFM
-9==             EDSTQSSIFTYTNSNST---RGPFE------GPNY-HIA------PRWVYHLTS---VWM
-10==            EDSTQSSIFTYTNSNST---RGPFE------GPNY-HIA------PRWVYHLTS---VWM
+14==            ARL-----SAETRLLGWNVPPEELRHI-PEHWLTYPEPPESMNYLLG--TLYIF-----F
+15==            ARL-----SAESRLLGWNVPPDELRHI-PEHWLIYPEPPESMNYLLG--TLYIF-----F
+16==            -GN-----GDLQFL-GWNVPPDQIQYI-PEHWLTQLEPPASMHYMLGVFYIFLF------
+17==            -SG-----SDELQFLGWNVPPDQIQYI-PEHWLTQLEPPASMHYMLGVFYIFLF------
+18==            FGYPEGV-SIV-DF--VRPEIKPYVHQ-HWYNYPP-VNP-MWHYLLGV---IYL-----F
+19==            FGYPEGMTVADFVP--DR---VKHMVL-DHWYNYPPVNP-MWHYLLGV---VYL-----F
+20==            -VV----DKVTPD---MA---HLISP---YWNQFPAMDPIWAKILTA--Y-MI------M
+21==            -VV----DKVTPD---MA---HLISP---YWNQFPAMDPIWAKILTA--Y-MI------M
+22==            -VV----DKVTPD---MA---HLISP---YWDQFPAMDPIWAKILTA--Y-MI------I
+23==            -SV---LDNVLPD---MA---HLVNP---YWSRFAPMDP-MMSKILGLFTLAI------M
+24==            -SV---LDNVLPD---MA---PLVNP---HWSRFAPMDP-TMSKILGLFTLVI------L
+25==            -NN---QTVVDKVP-PDML--HLIDA---NWYQYPPLNP-MWHGILGF---VIG-----M
+26==            -VV---DTMPKEML--YM-----IHE---HWYAFPPMNP-LWYSILGV---AMI-----I
+27==            -STTL---VNQTWW--YNPT-V-DIHP-HWAKFDPIPDAVYYSV--GIFIGVV-------
+28==            -RDLR---DNETWW--YNP--SIVVHP-HWREFDQVPDAVYYSL--GIFIGIC-------
+9==             -DSTQS--SIFTYTNSNS---TRGPFEGPNYHIAPRWVYHLTSVW-MI-----------F
+10==            -DSTQS--SIFTYTNSNS---TRGPFEGPNYHIAPRWVYHLTSVW-MI-----------F
 8=opsin_        ------------------------------------------------------------
-11==            DDTTRGSVFTYTNTNNT---RGPFE------GPNY-HIA------PRWVYNLVS---FFM
-12==            EDTTRDSVFTYTNSNNT---RGPFE------GPNY-HIA------PRWVYNLTS---VWM
-13==            ----MSSNSSQAPPNGT---PGPFD------GPQWPYQA------PQSTYVGVA---VLM
-30==            -----MPHLLSGFLEVTASPAPT----WDAPPDNVSGCGEQINYGRVEKVVIGS----IL
-31=p            -----MPHLLSGFLEVTASPAPT----WDAPPDNVSGCGEQINYGRVEKVVIGS----IL
-29==            VAGSWAPHLLS---EVTASPAPT----WDAPPDNASGCGEQINYGRVEKVVIGS----IL
-32==            TTSPPAPFETGG--NTTGISDVTVS-YQ----------------------VITS---LLL
-33=p            TTASQEPFGTGG--NVTSISDVTFS-YQ----------------------VITS---LLL
-34==            SHSSRSRDNASA--NDTSATNMTDDRYW------------SLTVYSHEHLVLTS---VIL
-35=p            SHSSRSRDNASA--NDTSATNMTDDRYW------------SLTVYSHEHLVLTS---VIL
-36==            --------------NVTVVPNTT---WWQA----------SAPFDTPAALVRAAAKAVVL
+11==            -DDTTRG-SVFTYTNTNN---TRGPFEGPNYHIAPRWVYNL-VSFFMI-----------I
+12==            -EDTTRD-SVFTYTNSNN---TRGPFEGPNYHIAPRWVYNLTSVW-MI-----------F
+1==             -NKT-GLARSPYEYPQY----YLAE----PWKYSALAA---YMFFLI------------L
+2==             -NIT-GVVRSPFEQPQY----YLAE----PWQFSMLAA---YMFLLI------------V
+4=p             -NRT-GLVRSPFEYPQY----YLAE----PWQFKILAL---YLFFLM------------S
+5=p             -NRT-GLVRSPFEYPQY----YLAE----PWQFKLLAV---YMFFLI------------C
+3==             -NKT-GVVRSPFEYPQY----YLAE----PWK-YRLVC---CYIFFLI-----------S
+6==             -INNLSAYSPFL-VPQD----HLG------NQGIFMAM---SVFMFFI-----------F
+7==             -SV--GPWDGPQ----Y----HIAP----VWAFYLQAAFMGTVFLIGF-----------P
+13==            -NGTPGPFDGPQ----WP---YQAPQ---STY-VGVAVLMGTVVACAS-----------V
+30==            --VTASP-APTWDAPPDNVSGC-GEQI--NYGRVEKVV---IGSILTLITLL-------T
+31=p            --VTASP-APTWDAPPDNVSGC-GEQI--NYGRVEKVV---IGSILTLITLL-------T
+29==            --VTASP-APTWDAPPDNASGC-GEQI--NYGRVEKVV---IGSILTLITLL-------T
+32==            --SPGQ--GNNTT-SPPAPFETGGN----TTGI--SDV---TVS-YQVITSLLLGTLIFC
+33=p            --SFGQ--GNNTTASQEPFG-TGGN----VTSI--SDV---TFS-YQVITSLLLGTLIFC
+34==            NGSHSS--RSRDNASANDTSAT-NM----TDDR--YWSLTVYSHEHLVLTSVILGLFVLC
+35=p            NGSHSS--RSRDNASANDTSAT-NM----TDDR--YWSLTVYSHEHLVLTSVILGLFVLC
+36==            WNVTVV--PNTTWWQASAPFDTPAA----LVRAAAKAV--VLGLLILA-TVV--------
                                                                             
 
-14==            -FFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDF-MMMVK-TPIFIYNSFHQGY
-15==            -FFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDF-MMMIK-TPIFIYNSFHQGY
-16==            -FLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDL-IMCLK-APIF--NSFHRGF
-17==            -FLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDL-IMCLK-APIFIYNSFHRGF
-18==            -FLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTN-VPFFTYNCFSGG-
-19==            -FLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTN-FPPFCYNCFSGG-
-20==            -MIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLYFE--
-21==            -MIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLYFE--
-22==            -IIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLYFE--
-23==            -AIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVMIINFYYE--
-24==            -VILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVMIINFYYE--
-25==            GMLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCM-SPPMVINCYYE--
-26==            -ILGIICVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFM-MPTMTSNCFAE--
-27==            GVVGIIGILGNGVVIYLFSKTKSLQTPANMFIINLAMSDLSFSAINGFPLKTISAFMK--
-28==            GICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLVNGFPLMTISCFLK--
-1==             FFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFG-FTVTMYTSMNGY-
-2==             FLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGG-FTTTLYTSLHGY-
-4=p             FFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNLAVAGTIMVCFG-FTVTFYTAINGY-
-5=p             FFLICLGLPINGLTLICTAQHKKLRQPLNFILVNLAVAGAIMVCFG-FTVTFYTAINGY-
-3==             FFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFG-FTVTFYTAWNGY-
-6==             FFIFIGGASINILTILCTIQFKKLRSHLNYILVNLSIANLFVAIFG-SPLSFYSFFNRY-
-7==             GTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIFSVFPV-FVASCNGY-
-9==             IFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STISVVNQVYGY-
-10==            IFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STISIVNQVSGY-
-8=opsin_        --------------------------------------DLAETVIA-STISIVNQVSGY-
-11==            IIVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVA-STISVFNQIFGY-
-12==            IFVVAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIA-STISVINQISGY-
-13==            GTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLCG-SSVSLSNNINGF-
-30==            TLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDLIGG-
-31=p            TLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDLIGG-
-29==            TLITLLTIAGNCLVVISVCFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDLIGG-
-32==            GTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAALYQVLN--
-33=p            GTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAALYQVLN--
-34==            GLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVSEISK--
-35=p            GLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVSEISK--
-36==            GLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLV-MPLGAVYEVVQ--
-                                                      .         .           
-
-14==            A--LGHLGCQIFGIIGSYTGIAAGA-TNAFIAYDRFNVITRPMEG-K-MTHGKAIAMIIF
-15==            A--LGHLGCQIFGVIGSYTGIAAGA-TNAFIAYDRYNVITRPMEG-K-MTHGKAIAMIIF
-16==            AIYLGNTWCQIFASIGSYSGIGAGM-TNAAIGYDRYNVITKPMNR-N-MTFTKAVIMNII
-17==            A--LGNTWCQIFASIGSYSGIGAGM-TNAAIGYDRYNVITKPMNR-N-MTFTKAVIMNII
-18==            VWMFSPQYCEIYACLGAITGVC-SIWLLCMISFDRYNIICNGFNG-PKLTTGKAVVFALI
-19==            RWMFSGTYCEIYAALGAITGVC-SIWTLCMISFDRYNIICNGFNG-PKLTQGKATFMCGL
-20==            TWVLGPMMCDIYAGLGSAFG-CSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLALGKM--
-21==            TWVLGPMMCDIYAGLGSAFG-CSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLALGKIAY
-22==            TWVLGPMMCDIYAGLGSAFG-CSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLALGKIAY
-23==            TWVLGPLWCDIYAGCGSLFG-CVSIWSMCMIAFDRYNVIVKGING-TPMTIKTSIMKILF
-24==            TWVLGPLWCDIYAACGSLFG-CVSIWSMCMIAFDRYNVIVKGING-TPMTIKTSIMKIAF
-25==            TWVLGPLFCQIYAMLGSLFG-CGSIWTMTMIAFDRYNVIVKGLSG-KPLSINGALIRIIA
-26==            TWILGPFMCEVYGMAGSLFG-CASIWSMVMITLDRYNVIVRGMAA-APLTHKKATLLLLF
-27==            KWIFGKVACQLYGLLGGIFG-FMSINTMAMISIDRYNVIGRPMAASKKMSHRRAFLMIIF
-28==            KWIFGFAACKVYGFIGGIFG-FMSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFIMIIF
-1==             -FVFGPTMCSIEGFFATLGG-EVALWSLVVLAIERYIVICKPM-GNFRFGNTHAIMGVAF
-2==             -FVFGPTGCNLEGFFATLGG-EIGLWSLVVLAIERYVVVCKPM-SNFRFGENHAIMGVAF
-4=p             -FVLGPTGCAVEGFMATLGG-EVALWSLVVLAIERYIVVCKPM-GSFKFSSSHAFAGIAF
-5=p             -FALGPTGCAVEGFMATLGG-EVALWSLVVLAIERYIVVCKPM-GSFKFSSTHASAGIAF
-3==             -FVFGPVGCAVEGFFATLGG-QVALWSLVVLAIERYIVVCKPM-GNFRFSATHAMMGIAF
-6==             -FIFGATACKIEGFLATLGG-MVGLWSLAVVAFERWLVICKPL-GNFTFKTPHAIAGCIL
-7==             -FVFGRHVCALEGFLGTVAG-LVTGWSLAFLAFERYIVICKPF-GNFRFSSKHALTVVLA
-9==             -FVLGHPMCVLEGYTVSLCG-ITGLWSLAIISWERWMVVCKPF-GNVRFDAKLAIVGIAF
-10==            -FVLGHPMCVLEGYTVSLCG-ITGLWSLAIISWERWLVVCKPF-GNVRFDAKLAIVGIAF
-8=opsin_        -FVLGHPMCVLEGYTVSLCG-ITGLWSLAIISWERWLVVCKPF-GNVRFDAKLAIVGIAF
-11==            -FILGHPLCVIEGYVVSSCG-ITGLWSLAIISWERWFVVCKPF-GNIKFDSKLAIIGIVF
-12==            -FILGHPMCVVEGYTVSACG-ITALWSLAIISWERWFVVCKPF-GNIKFDGKLAVAGILF
-13==            -FVFGRRMCELEGFMVSLTG-IVGLWSLAILALERYVVVCKPL-GDFQFQRRHAVSGCAF
-30==            KWIFGHFFCNVFIAMDVMCC-TASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILS
-31=p            KWIFGHFFCNVFIAMDVMCC-TASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILS
-29==            KWIFGHFFCNVFIAMDVMCC-TASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILS
-32==            KWTLGQVTCDLFIALDVLCC-TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISL
-33=p            KWTLGQVTCDLFIALDVLCC-TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISL
-34==            VWFLHSEVCDMWISVDVLCC-TASILHLVAIAMDRYWAVTS-IDYIRRRSARRILLMIMV
-35=p            VWFLHSEVCDMWISVDVLCC-TASILHLVAIAMDRYWAVTS-IDYIRRRSARRILLMIMV
-36==            RWTLGPELCDMWTSGDVLCC-TASILHLVAIALDRYWAVTN-IDYIHASTAKRVGMMIAC
-                   :    * :                   :  :*:  :   :                 
+14==            TL--M--SMLGNGLVIWV--FSAA--KSLRTPSNILVINLAFCDFMMM-VKTPIFIYNSF
+15==            TV--I--SMIGNGLVMWV--FSAA--KSLRTPSNILVINLAFCDFMMM-IKTPIFIYNSF
+16==            CA--STVGN-GMVIWIFS--TS----KSLRTPSNMFVLNLAVFDLIMC-LKAPIF--NSF
+17==            FA--STLGN-GMVIWIFS--TS----KSLRTPSNMFVLNLAVFDLIMC-LKAPIFIYNSF
+18==            LGT-V-SIF-GNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTNV-PFFTY---NCF
+19==            LG--VISIA-GNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTNF-PPFCY---NCF
+20==            IGMISWCGN-GVVIYIFATTKSLR--TPANLLVINLAISDF---GIMI-TNTPMMGINLY
+21==            IGMISWCGN-GVVIYIFATTKSLR--TPANLLVINLAISDF---GIMI-TNTPMMGINLY
+22==            IGMISWCGN-GVVIYIFATTKSLR--TPANLLVINLAISDF---GIMI-TNTPMMGINLY
+23==            IIS-C-CGN-GVVVYIFGGTKSLR--TPANLLVLNLAFSDFCMMA-SQ--SP-VMIINFY
+24==            IIS-C-CGN-GVVVYIFGGTKSLR--TPANLLVLNLAFSDFCMMA-SQ--SP-VMIINFY
+25==            LGFVSAMGN-GMVVYIFLSTKSLR--TPSNLFVINLAISNFLMMFCM---SPPMVI-NCY
+26==            LGIICVLGN-GMVIYLMMTTKSLR--TPTNLLVVNLAFSDFCMMAFM---MPTM---TSN
+27==            -GIIGILGN-GVVIYLFSKTKSLQ--TPANMFIINLA-MS-DLSFSAI-NGFPL---KTI
+28==            -GIIGCGGN-GIVIYLFTKTKSLQ--TPANMFIINLAFSDFTFSLVN--GFPLM---TIS
+9==             VVIASVFTN-GLVLAATMKFKKLR--HPLNWILVNLAVADLAETVIASTIS----V-VNQ
+10==            VVTASVFTN-GLVLAATMKFKKLR--HPLNWILVNLAVADLAETVIASTIS----I-VNQ
+8=opsin_        ---------------------------------------DLAETVIASTIS----I-VNQ
+11==            VVIASCFTN-GLVLVATAKFKKLR--HPLNWILVNLAFVDLVETLVASTIS----V-FNQ
+12==            VVAASVFTN-GLVLVATWKFKKLR--HPLNWILVNLAVADLGETVIASTIS----V-INQ
+1==             VGFPV---N-FLTLFVTVQHKKLR--TPLNYILLNLAM-A--NLFMVL-FGFTVTM-YTS
+2==             LGFPI---N-FLTLYVTVQHKKLR--TPLNYILLNLAV-A--DLFMVF-GGFTTTL-YTS
+4=p             MGLPI---N-GLTLVVTAQHKKLR--QPLNFILVNLAV-A--GTIMVC-FGFTVTF-YTA
+5=p             LGLPI---N-GLTLICTAQHKKLR--QPLNFILVNLAV-A--GAIMVC-FGFTVTF-YTA
+3==             TGLPI---N-LLTLLVTFKHKKLR--QPLNYILVNLAV-A--DLFMAC-FGFTVTF-YTA
+6==             IGGASI--N-ILTILCTIQFKKLR--SHLNYILVNL-SIA--NLFVAIFGSPLSFY-SFF
+7==             LNAMVL--V-A-----TLRYKKLR--QPLNYILVN-VSFG--GFLLCIFSVFPVFVASC-
+13==            VNGLVI--V-V---SIC--YKKLR--SPLNYILVNLAVADLLVTLCGS-SV----SLSNN
+30==            ---IAGN-CLVVISVSFVK--KLRQ--PSNYLIVSLALADLSVAVAVMPFV-----SVTD
+31=p            ---IAGN-CLVVISVSFVK--KLRQ--PSNYLIVSLALADLSVAVAVMPFV-----SVTD
+29==            ---IAGN-CLVVISVCFVK--KLRQ--PSNYLIVSLALADLSVAVAVMPFV-----SVTD
+32==            AVLGNAC-VVAA-IALERSLQNVA-----NYLIGSLAV-TDLMVSVLVLPMA----ALYQ
+33=p            AVLGNAC-VVAA-IALERSLQNVA-----NYLIGSLAV-TDLMVSVLVLPMA----ALYQ
+34==            -CIIGNCFVIAA-VMLERSLHNVA-----NYLILSLAVADLMVAVLVMPLSV----VSEI
+35=p            -CIIGNCFVIAA-VMLERSLHNVA-----NYLILSLAVADLMVAVLVMPLSV----VSEI
+36==            ----GNVFVIAA-ILLERHLRSAA-----NNLILSLAVADLLVACLVMPLGA----VYEV
+                                                                            
 
-14==            IYMYATPWV-VACYTETW------GRFVPEGYLTSCTFDYLT--DNFDTRLFVACIFFFS
-15==            IYLYATPWV-VACYTESW------GRFVPEGYLTSCTFDYLT--DNFDTRLFVACIFFFS
-16==            IWLYCTPWV-VLPLTQFW------DRFVPEGYLTSCSFDYLS--DNFDTRLFVGTIFFFS
-17==            IWLYCTPWV-VLPLTQFW------DRFVPEGYLTSCSFDYLS--DNFDTRLFVGTIFLFS
-18==            SWVIAIGCA-LPPFF-GW------GNYILEGILDSCSYDYLT--QDFNTFSYNIFIFVFD
-19==            AWVISVGWS-LPPFF-GW------GSYTLEGILDSCSYDYFT--RDMNTITYNICIFIFD
-20==            --------------------------YVPEGNLTSCGIDYLE--RDWNPRSYLIFYSIFV
-21==            IWFMSSIWC-LAPAF-GW------SRYVPEGNLTSCGIDYLE--RDWNPRSYLIFYSIFV
-22==            IWFMSTIWCCLAPVF-GW------SRYVPEGNLTSCGIDYLE--RDWNPRSYLIFYSIFV
-23==            IWMMAVFWT-VMPLI-GW------SAYVPEGNLTACSIDYMT--RMWNPRSYLITYSLFV
-24==            IWMMAVFWT-IMPLI-GW------SSYVPEGNLTACSIDYMT--RQWNPRSYLITYSLFV
-25==            IWLFSLGWT-IAPMF-GW------NRYVPEGNMTACGTDYFN--RGLLSASYLVCYGIWV
-26==            VWIWSGGWT-ILPFF-GW------SRYVPEGNLTSCTVDYLT--KDWSSASYVVIYGLAV
-27==            VWMWSIVWS-VGPVF-NW------GAYVPEGILTSCSFDYLS--TDPSTRSFILCMYFCG
-28==            VWLWSVLWA-IGPIF-GW------GAYTLEGVLCNCSFDYIS--RDSTTRSNILCMFILG
-1==             TWIMALACA-APPLV-GW------SRYIPEGMQCSCGPDYYTLNPNFNNESYVVYMFVVH
-2==             TWVMALACA-APPLV-GW------SRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVH
-4=p             TWVMALACA-APPLF-GW------SRYIPEGMQCSCGPDYYTLNPDYNNESYVIYMFVCH
-5=p             TWVMAMACA-APPLV-GW------SRYIPEGIQCSCGPDYYTLNPEYNNESYVLYMFICH
-3==             TWVMAFSCA-APPLF-GW------SRYMPEGMQCSCGPDYYTHNPDYHNESYVLYMFVIH
-6==             PWISALAAS-LPPLF-GW------SRYIPEGLQCSCGPDWYTTNNKYNNESYVMFLFCFC
-7==             TWTIGIGVS-IPPFF-GW------SRFIPEGLQCSCGPDWYTVGTKYRSESYTWFLFIFC
-9==             SWIWAAVWT-APPIF-GW------SRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTC
-10==            SWIWSAVWT-APPIF-GW------SRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTC
-8=opsin_        SWIWAAVWT-APPIF-GW------SRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTC
-11==            SWVWAWGWS-APPIF-GW------SRYWPHGLKTSCGPDVFSGSVELGCQSFMLTLMITC
-12==            SWLWSCAWT-APPIF-GW------SRYWPHGLKTSCGPDVFSGSSDPGVQSYMVVLMVTC
-13==            TWGWALLWS-APPLL-GW------SSYVPEGLRTSCGPNWYTGGS--NNNSYILSLFVTC
-30==            VWLLSASIT-LPPLF-GW-----AQNVNDDKV---CLIS--------QDFGYTIYSTAVA
-31=p            VWLLSASIT-LPPLF-GW-----AQNVNDDKV---CLIS--------QDFGYTIYSTAVA
-29==            VWLLSASIT-LPPLF-GW-----AQNVNDDKV---CLIS--------QDFGYTIYSTAVA
-32==            TWLIGFLIS-IPPML-GWRTPE--DRSDPDA----CTIS--------KDHGYTIYSTFGA
-33=p            TWLIGFLIS-IPPML-GWRTPE--DRSDPDA----CTIS--------KDHGYTIYSTFGA
-34==            VWIVALFIS-IPPLF-GWRDPN-N---DPDKTG-TCIIS--------QDKGYTIFSTVGA
-35=p            VWIVALFIS-IPPLF-GWRDPN-N---DPDKTG-TCIIS--------QDKGYTIFSTVGA
-36==            VWTVSFFVC-IAQLL-GWKDPDWNQRVSEDL---RCVVS--------QDVGYQIFATASS
-                                             .     *  .                     
+14==            HQG--YA---LG---HLGC-QIFGI--IGSYTGIAA--GATN-AFIA--YDRFNVITRPM
+15==            HQG--YA---LG---HLGC-QIFGV--IGSYTGIAA--GATN-AFIA--YDRYNVITRPM
+16==            HRG--FAIYLGN---TW-C-QIFAS--IGSYSGIGA--GMTN-AAIG--YDRYNVITKPM
+17==            HRG--FA--LGN---TW-C-QIFAS--IGSYSGIGA--GMTN-AAIG--YDRYNVITKPM
+18==            SGG-VWMF---SPQYCEIY-ACLGA--ITGVCSI-WLLCMISFD--R--YNIICN--GFN
+19==            SGG-RWMF---SGTYCEIY-AALGA--ITGVCSI-WTLCMISFD--R--YNIICN--GFN
+20==            FE---TWV--LGPMMCDIY-AGLGS--AFGCSSI-W--SMCMISLDR--YQVIVK--G-M
+21==            FE---TWV--LGPMMCDIY-AGLGS--AFGCSSI-W--SMCMISLDR--YQVIVK--G-M
+22==            FE---TWV--LGPMMCDIY-AGLGS--AFGCSSI-W--SMCMISLDR--YQVIVK--G-M
+23==            YE---TWV--LGPLWCDIY-AGCGS--LFGCVSI-W--SMCMIAFDR--YNVIVK--G-I
+24==            YE---TWV--LGPLWCDIY-AACGS--LFGCVSI-W--SMCMIAFDR--YNVIVK--G-I
+25==            YE---TWV--LGPLFCQIY-AMLGS--LFGCGSI-W--TMTMIAFDR--YNVIVK--GLS
+26==            CFA-ETWI--LGPFMCEVY-GMAGS--LFGCASI-W--SMVMITLDR--YNVIVR--G-M
+27==            SAFMKKWI--FGKVACQLY-GLLGG--IFGFMSI-NTMAMISID--R--YNVIGRPMA-A
+28==            CFL-KKWI--FGFAACKVY-GFIGG--IFGFMSI-MTMAMISID--R--YNVIGRPMA-A
+9==             VYG--YFV--LGHPMCV---L-EG--YTVSLC-GIT--GLWSLAIIS--WERWMVVCKPF
+10==            VSG--YFV--LGHPMCV---L-EG--YTVSLC-GIT--GLWSLAIIS--WERWLVVCKPF
+8=opsin_        VSG--YFV--LGHPMCV---L-EG--YTVSLC-GIT--GLWSLAIIS--WERWLVVCKPF
+11==            IFG--YFI--LGHPLCVIE-G-YV--V-SS-C-GIT--GLWSLAIIS--WERWFVVCKPF
+12==            ISG--YFI--LGHPMCV---V-EG--YTVSAC-GIT--ALWSLAIIS--WERWFVVCKPF
+1==             MNG--YFV--FGPTMCSIE-GFFA--TLGGEV-ALW--SLVVLAIER--Y---IVICKPM
+2==             LHG--YFV--FGPTGCNLE-GFFA--TLGGEI-GLW--SLVVLAIER--Y---VVVCKPM
+4=p             ING--YFV--LGPTGCAVE-GFMA--TLGGEV-ALW--SLVVLAIER--Y---IVVCKPM
+5=p             ING--YFA--LGPTGCAVE-GFMA--TLGGEV-ALW--SLVVLAIER--Y---IVVCKPM
+3==             WNG--YFV--FGPVGCAVE-GFFA--TLGGQV-ALW--SLVVLAIER--Y---IVVCKPM
+6==             -NR--YFI--FGATACKIE-GFLA--TLGGMV-GLW--SLAVVAFER--W---LVICKPL
+7==             -NG--YFV--FGRHVCALE-GFLG--TVAGLVTG-W--SLAFLAFER--Y---IVICKPF
+13==            ING--FFV--FGRRMCELE-GFMVSLT--GIV-GLW--SLAILALER--Y---VVVCKPL
+30==            LIG-GKWIFGHFFCNVFI--AMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCM
+31=p            LIG-GKWIFGHFFCNVFI--AMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCM
+29==            LIG-GKWIFGHFFCNVFI--AMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCM
+32==            VLN-KWT---LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPR-R
+33=p            VLN-KWT---LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPR-R
+34==            S-K-VWFLHSEV-CDMWIS-V-DVLCCTASILHLVAIAMDRYWAVTSI-DYIRRR--S-A
+35=p            S-K-VWFLHSEV-CDMWIS-V-DVLCCTASILHLVAIAMDRYWAVTSI-DYIRRR--S-A
+36==            VQR-WTL--GPELCDMWTS-G-DVLCCTASILHLVAIALDRYWAVTNI-DYIHASTAK-R
+                                                                            
 
-14==            FVCPTTMITYYYSQIVGHVFSHEKAL----------------------------------
-15==            FVCPTTMITYYYSQIVGHVFSHEKAL----------------------------------
-16==            FVCPTLMILYYYSQIVGHVFSHEKAL----------------------------------
-17==            FVVPTLMILYYYSQIVGHVFNHEKAL----------------------------------
-18==            YFLPAAIIVFSYVFIVKAIFAHEAAM----------------------------------
-19==            FFLPASVIVFSYVFIVKAIFAHEAAM----------------------------------
-20==            YYIPLFLICYSYWFIIAAVSAHEKAM----------------------------------
-21==            YYIPLFLICYSYWFIIAAVSAHEKAM----------------------------------
-22==            YYIPLFLICYSYWFIIAAVSAHEKAM----------------------------------
-23==            YYTPLFLICYSYWFIIAAVAAHEKAM----------------------------------
-24==            YYTPLFMICYSYWFIIATVAAHEKAM----------------------------------
-25==            YFVPLFLIIYSYWFIIQAVAAHEKNM----------------------------------
-26==            YFLPLITMIYCYFFIVHAVAEHEKQL----------------------------------
-27==            FMLPIIIIAFCYFNIVMSVSNHEKEM----------------------------------
-28==            FFGPILIIFFCYFNIVMSVSNHEKEM----------------------------------
-1==             FLVPFVIIFFCYGRLLCTV-----------------------------------------
-2==             FTIPMIVIFFCYGQLVFTV-----------------------------------------
-4=p             FILPVAVIFFTYGRLVCTV-----------------------------------------
-5=p             FILPVTIIFFTYGRLVCTV-----------------------------------------
-3==             FIIPVVVIFFSYGRLICKV-----------------------------------------
-6==             FAVPFGTIVFCYGQLLITL-----------------------------------------
-7==             FIVPLSLICFSYTQLLRAL-----------------------------------------
-9==             CITPLSIIVLCYLQVWLAI-----------------------------------------
-10==            CIIPLAIIMLCYLQVWLAI-----------------------------------------
-8=opsin_        CITPLSIIVLCYLQVWLAI-----------------------------------------
-11==            CFLPLFIIIVCYLQVWMAI-----------------------------------------
-12==            CFFPLAIIILCYLQVWLAI-----------------------------------------
-13==            FVLPLSLILFSYTNLLLTL-----------------------------------------
-30==            FYIPMSVMLFMYYQIYKAARKSAAK--HKF-------------------P----------
-31=p            FYIPMSVMLFMYYQIYKAARKSAAK--HKF-------------------P----------
-29==            FYIPMSVMLFMYYQIYKAARKSAAK--HKF-------------------P----------
-32==            FYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADTRHGASP----APQPKKS----VN
-33=p            FYIPLLLMLVLYGRIFRAARFRIRKTVRKVEKKGAGTSLGTSS----APPPKKS----LN
-34==            FYLPMLVMMIIYIRIWLVARSRIRK--DKFQ--MTKARLKTEETTLVASPKTEY--SVVS
-35=p            FYLPMLVMMIIYIRIWLVARSRIRK--DKFQ--MTKARLKTEETTLVASPKTEY--SVVS
-36==            FYVPVLIILILYWRIYQTARKRIRR--RR----GATARGG------VGPPPVPAGGALVA
-                   *   :   *  :                                             
+14==            EGK-MT--HGKAI-AMII-FIYMYA--TPWVVACYTET------WGRF---VPEGYLT--
+15==            EGK-MT--HGKAI-AMII-FIYLYA--TPWVVACYTES------WGRF---VPEGYLT--
+16==            NRN-MTFTKAVI--MNII-IWLYC---TPWVVLPLTQF------WDRF---VPEGYLT--
+17==            NRN-MTFTKAVI--MNII-IWLYC---TPWVVLPLTQF------WDRF---VPEGYLT--
+18==            GPK---LTTGKA--VVF---ALISW-VIAIGCALPPFF-----GW-GN---YILEGIL--
+19==            GPK---LTQGKATFMC-------GL-AWVISVGWSLPPF---FGW-GS---YTLEGIL--
+20==            AG-------RPMTIPL----ALGK----------------------MY---VPEGNLT--
+21==            AG-------RPMTIPL----ALGKI-AYIWFMSSIWCL-APAFGWSRY---VPEGNLT--
+22==            AG-------RPMTIPL----ALGKI-AYIWFMSTIWCCLAPVFGWSRY---VPEGNLT--
+23==            NGTPMTIKTSIMKILFIW--MMAVF-WTVMPLI----------GWSAY---VPEGNLT--
+24==            NGTPMTIKTSIMKIAFIW--MMAVF-WTIMPLI----------GWSSY---VPEGNLT--
+25==            GKPLS---INGALIRIIA-IWLFSLGWTIAPMF----------GWNRY---VPEGNMT--
+26==            AA--APLTHKKATLLLLF-VWIWSGGWTILPFF----------GWSRY---VPEGNLT--
+27==            SKKMS---HRRAFLMIIF-VWMWSI---VWSVGPVF-------NWGAY---VPEGILT--
+28==            SKKMS---HRRAFIMIIF-VWLWS-----VLWAIGPIF-----GWGAY---TLEGVLC--
+9==             GNVRF--DAKLAI-VGIAFSWIWAAVWTAPPI----------FGWSRY---WPHGLKT--
+10==            GNVRF--DAKLAI-VGIAFSWIWSAVWTAPPI----------FGWSRY---WPHGLKT--
+8=opsin_        GNVRF--DAKLAI-VGIAFSWIWAAVWTAPPI----------FGWSRY---WPHGLKT--
+11==            GNIKF--DSKLAI-IGIVFSW---VWAWGWSAPPI-------FGWSRY---WPHGLKT--
+12==            GNIKF--DGKLAV-AGILFSWLWSCAWTAPPI----------FGWSRY---WPHGLKT--
+1==             GNFRF--GNTHAI-MG---VAFTWIMA-LACAAPPL------VGWSRY---IPEGMQC--
+2==             SNFRF--GENHAI-MG---VAFTWVMA-LACAAPPL------VGWSRY---IPEGMQC--
+4=p             GSFKF--SSSHAF-AG---IAFTWVMA-LACAAPPL------FGWSRY---IPEGMQC--
+5=p             GSFKF--SSTHAS-AG---IAFTWVMA-MACAAPPL------VGWSRY---IPEGIQC--
+3==             GNFRF--SATHAM-MG---IAFTWVMAFS-CAAPPL------FGWSRY---MPEGMQC--
+6==             GNFTF--KTPHAI-AG---CILPWISALAASLPPLF-------GWSRY---IPEGLQC--
+7==             GNFRF--SSKHALTVV---LATWTI-GIGVSIPPFF-------GWSRF---IPEGLQC--
+13==            GDFQFQ-RRHAVS--G---CAFTWGWALLWSAPPLL-------GWSSY---VPEGLRT--
+30==            AK---MILSVWLLS-A---SITLPPLFGWAQNVNDDKVCLI-SQDFGYTIYSTAVAFYIP
+31=p            AK---MILSVWLLS-A---SITLPPLFGWAQNVNDDKVCLI-SQDFGYTIYSTAVAFYIP
+29==            AK---MILSVWLLS-A---SITLPPLFGWAQNVNDDKVCLI-SQDFGYTIYSTAVAFYIP
+32==            AA---ALISLTWLI-GFLISIPPMLGWRTPEDRSDPDACTI-SKDHGYTIYSTFGAFYIP
+33=p            AA---ALISLTWLI-GFLISIPPMLGWRTPEDRSDPDACTI-SKDHGYTIYSTFGAFYIP
+34==            RRILLMIMVVWIV--ALFISIPPLFGWRDPNNDPDKTGTCIISQDKGYTIFSTVGAFYLP
+35=p            RRILLMIMVVWIV--ALFISIPPLFGWRDPNNDPDKTGTCIISQDKGYTIFSTVGAFYLP
+36==            VGMMIA-CVWTVSFFV---CIAQLLGWKDPDWNQRV------SEDLRC-VVSQDVGYQIF
+                                                                            
 
-14==            ----------------------------RDQAKKM----------------NVES-----
-15==            ----------------------------RDQAKKM----------------NVDS-----
-16==            ----------------------------REQAKKM----------------NVES-----
-17==            ----------------------------REQAKKM----------------NVES-----
-18==            ----------------------------RAQAKKM----------------NVST-----
-19==            ----------------------------RAQAKKM----------------NVTN-----
-20==            ----------------------------REQAKKM----------------NVKS-----
-21==            ----------------------------REQAKKM----------------NVKS-----
-22==            ----------------------------REQAKKM----------------NVKS-----
-23==            ----------------------------REQAKKM----------------NVKS-----
-24==            ----------------------------RDQAKKM----------------NVKS-----
-25==            ----------------------------REQAKKM----------------NVAS-----
-26==            ----------------------------REQAKKM----------------NVAS-----
-27==            ----------------------------AAMAKRL----------------NAKE-----
-28==            ----------------------------AAMAKRL----------------NAKE-----
-1==             ----------------------------KEAAAA--------------------------
-2==             ----------------------------KEAAAQ--------------------------
-4=p             ----------------------------KAAAAQ--------------------------
-5=p             ----------------------------KAAAAQ--------------------------
-3==             ----------------------------REAAAQ--------------------------
-6==             ----------------------------KLAAKA--------------------------
-7==             ----------------------------KAVAAQ--------------------------
-9==             ----------------------------RAVAKQ--------------------------
-10==            ----------------------------RAVAKQ--------------------------
-8=opsin_        ----------------------------RAVAKQ--------------------------
-11==            ----------------------------RAVAAQ--------------------------
-12==            ----------------------------RAVAAQ--------------------------
-13==            ----------------------------RAAAAQ--------------------------
-30==            ------------------------G-FPRVQ---------PESVISLNGVVKLQK-----
-31=p            ------------------------G-FPRVQ---------PESVISLNGVVKLQK-----
-29==            ------------------------G-FPRVE---------PDSVIALNGIVKLQK-----
-32==            GESGSRNWRLGVESKAGGALCAN-G-AVRQGDDGAALEVIE-----VHRVGNSKEHLPL-
-33=p            GQPGSGDWRRCAENRAVGTPCTN-G-AVRQGDDEATLEVIE-----VHRVGNSKEHLPL-
-34==            DCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSSSERLKQI
-35=p            DCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSSSERLKQI
-36==            ---GGGSGGIAA------AVVAVIG---RP---------LP----------TISE-----
+14==            --SC--TF-DYLT-------DN-FDTRLF-----VACIFFF--SF---------VC----
+15==            --SC--TF-DYLT-------DN-FDTRLF-----VACIFFF--SF---------VC----
+16==            --SCSFDY-LS---------DN-FDTRLF-----VGTIFFF--SF---------VC----
+17==            --SCSFDY-LS---------DN-FDTRLF-----VGTIFLF--SF---------VV----
+18==            --DSC-SY-DYLT-------QD-FNTF-S-----Y-NIFIF--VF---------DY--FL
+19==            --DSC-SY-DYFT-------RD-MNTITY-----NICIFIF--DFFLP------AS----
+20==            --SC--GI-DYLE-------RD-WNPR-S-----YLIFY----SIF--------VY-YIP
+21==            --SC--GI-DYLE-------RD-WNPR-S-----YLIFY----SIF--------VY-YIP
+22==            --SC--GI-DYLE-------RD-WNPR-S-----YLIFY----SIF--------VY-YIP
+23==            --AC--SI-DYMT-------RM-WNPR-S-----YLITY----SLF--------VY-YTP
+24==            --AC--SI-DYMT-------RQ-WNPR-S-----YLITY----SLF--------VY-YTP
+25==            --AC--GT-DYFN-------RG-LLSA-S-----YLVCY----GIW--------VYFVPL
+26==            --SCT-V--DYLT-------KD-WSSA-S-----YVVIY----GLA--------VY---F
+27==            --SCSFDYLSTDP-------ST-RSFILC-----M-YFC----GFMLPIIIIAFCY----
+28==            --NCSFDYIS-RD-------STTRSNILC-----M-FIL----GFFGPILIIFFCY----
+9==             --SCGPDVFS--G-------SSYPGVQSY-----MIVLMVT--CCITPLSIIVLCYLQ--
+10==            --SCGPDVFS--G-------SSYPGVQSY-----MIVLMVT--CCIIPLAIIMLCYLQ--
+8=opsin_        --SCGPDVFS--G-------SSYPGVQSY-----MIVLMVT--CCITPLSIIVLCYLQ--
+11==            --SCGPDVFS--G-------SVELGCQSF-----MLTLMIT--CCFLPLFIIIVCYLQ--
+12==            --SCGPDVFS--G-------SSDPGVQSY-----MVVLMVT--CCFFPLAIIILCYLQ--
+1==             --SCGPDY-YTLN-------PNF-NNESY-----VVYMFVV--HFLVPFVIIFFCY----
+2==             --SCGIDY-YTLK-------PEV-NNESF-----VIYMFVV--HFTIPMIVIFFCY----
+4=p             --SCGPDY-YTLN-------PDY-NNESY-----VIYMFVC--HFILPVAVIFFTY----
+5=p             --SCGPDY-YTLN-------PEY-NNESY-----VLYMFIC--HFILPVTIIFFTY----
+3==             --SCGPDY-YTHN-------PDY-HNESY-----VLYMFVI--HFIIPVVVIFFSY----
+6==             --SCGPDW-YTTN-------NKY-NNESY-----VMFLFCF--CFAVPFGTIVFCY----
+7==             --SCGPDW-YTVG-------TKY-RSESYT----WFLFIFC--FIVPLSLICFSYTQLL-
+13==            --SCGPNW-YT-G-------GSN-NNSYIL----SLFVTCF--VLPL-SLILFSYT----
+30==            MSVMLFMYYQIYK----AARKSAAKHKFP--GFPRVQPE---SVISLN------GV-VKL
+31=p            MSVMLFMYYQIYK----AARKSAAKHKFP--GFPRVQPE---SVISLN------GV-VKL
+29==            MSVMLFMYYQIYK----AARKSAAKHKFP--GFPRVEP----DS-VIAL-----NGIVKL
+32==            LLLMLVLYGRIFR----AARFRIRKTVKKVEKTGADT------RHGASPAPQPKKSVNGE
+33=p            LLLMLVLYGRIFR----AARFRIRKTVRKVEKKGAGT------SLGTSSAPPPKKSLNGQ
+34==            MLVMMIIYIRIWL---VAR-SRIRKDKFQMTK-ARLKTEETTLVASPK---TEYSVVSDC
+35=p            MLVMMIIYIRIWL---VAR-SRIRKDKFQMTK-ARLKTEETTLVASPK---TEYSVVSDC
+36==            ATASSFYVPVLIILILYWRIYQTARKRIRR-R-RGAT-----ARGGVG---PPPVPAGG-
                                                                             
 
-14==            ---------------------LRSNV-DKNKE----------------------------
-15==            ---------------------LRSNV-DKSKE----------------------------
-16==            ---------------------LRSNV-DKSKE----------------------------
-17==            ---------------------LRSNV-DKSKE----------------------------
-18==            ---------------------LRSNEADAQR-----------------------------
-19==            ---------------------LRSNEAETQR-----------------------------
-20==            ---------------------LRSSE-DAEK-----------------------------
-21==            ---------------------LRSSE-DAEK-----------------------------
-22==            ---------------------LRSSE-DADK-----------------------------
-23==            ---------------------LRSSE-DCDK-----------------------------
-24==            ---------------------LRSSE-DCDK-----------------------------
-25==            ---------------------LRSSE-NQNT-----------------------------
-26==            ---------------------LRANA-DQQKQ----------------------------
-27==            ---------------------LRKAQ---AGA----------------------------
-28==            ---------------------LRKAQ---AGA----------------------------
-1==             ----------------------QQESASTQK-----------------------------
-2==             ----------------------QQESATTQK-----------------------------
-4=p             ----------------------QQDSASTQK-----------------------------
-5=p             ----------------------QQDSASTQK-----------------------------
-3==             ----------------------QQESATTQK-----------------------------
-6==             ----------------------QADSASTQK-----------------------------
-7==             ----------------------QQESATTQK-----------------------------
-9==             ----------------------QKESESTQK-----------------------------
-10==            ----------------------QKESESTQK-----------------------------
-8=opsin_        ----------------------QKESESTQK-----------------------------
-11==            ----------------------QKESESTQK-----------------------------
-12==            ----------------------QKESESTQK-----------------------------
-13==            ----------------------QKEADTTQR-----------------------------
-30==            ---------------------EVEECAN------------------------LSRLLKHE
-31=p            ---------------------EVEECAN------------------------LSRLLKHE
-29==            ---------------------EVEECAN------------------------LSRLLKHE
-32==            ---PSEAGPTPCA----PASFERKNERNAEA----------------------KR-----
-33=p            ---PSESGSNSYA----PACLERKNERNAEA----------------------KR-----
-34==            QIETAEAFANGCAEEASIAMLERQ-CNNGKKISSNDTP---Y---------SRTR----E
-35=p            QIETAEAFANGCAEEASIAMLERQ-CNNGKKISSNDTP---Y---------SRTR----E
-36==            --TTTTGFTNVSSNNTSP---EKQSCANGLE---ADPPTTGYGAVAAAYYPSLVRRKPKE
+14==            -----PTTMITYY-YSQIVGH--VFS-HEK--------AL---RDQAKKMN-VESLRS--
+15==            -----PTTMITYY-YSQIVGH--VFS-HEK--------AL---RDQAKKMN-VDSLRS--
+16==            -----PTLMILYY-YSQIVGH--VFS-HEK--------AL---REQAKKMN-VESLRS--
+17==            -----PTLMILYY-YSQIVGH--VFN-HEK--------AL---REQAKKMN-VESLRS--
+18==            PA---AIIVF-SY-VFI-VKAIFA-HEA----------AM---RAQAKKMN-VSTLRS--
+19==            -V---I--VF-SY-VFI-VKAIFA-HEA----------AM---RAQAKKMN-VTNLRS--
+20==            LF---LICY--SY-WFIIA-A--VSA-HEK--------AM---REQAKKMN-VKSLRS--
+21==            LF---LICY--SY-WFIIA-A--VSA-HEK--------AM---REQAKKMN-VKSLRS--
+22==            LF---LICY--SY-WFIIA-A--VSA-HEK--------AM---REQAKKMN-VKSLRS--
+23==            LF---LICY--SY-WFIIAAV--A-A-HEK--------AM---REQAKKMN-VKSLRS--
+24==            LF---MICY--SY-WFIIATV--A-A-HEK--------AM---RDQAKKMN-VKSLRS--
+25==            FL---IIYS--YW-FIIQA-V--A-A-HEK--------NM---REQAKKMN-VASLRS--
+26==            LP---LITMI-YC-YFFIV-H--AVAEHEK--------QL---REQAKKMN-V---ASL-
+27==            -F---NIVMSVSN-HEKEMAAM-AKRLNAKELRKAQ-AGA---SAEMKLAKIS---MVII
+28==            -F---NIVMSVSN-HEKEMAAM-AKRLNAKELRKAQ-AGA---NAEMRLAKISIVIVSQF
+9==             -------VWLAI---RAVA-KQ-QKESESTQ------KAE---KE-VTRMVVVMVLA---
+10==            -------VWLAI---RAVA-KQ-QKESESTQ------KAE---KE-VTRMVVVMIFA---
+8=opsin_        -------VWLAI---RAVA-KQ-QKESESTQ------KAE---KE-VTRMVVVMVLA---
+11==            -------VWMAI---RAVA-AQ-QKESESTQ------KAE---RE-V-SRMVVVMIV---
+12==            -------VWLAI---RAVA-AQ-QKESESTQ------KAE---KE-V-SRMVVVMIV---
+1==             -------GRLLCT-VKEAA-AA-QQESASTQ------KAE---KE-VTRMVVLMVIGFLV
+2==             -------GQLVFT-VKEAA-AQ-QQESATTQ------KAE---KE-VTRMVIIMVIFFLI
+4=p             -------GRLVCT-VKAAA-AQ-QQDSASTQ------KAE---RE-VTKMVILMVFGF-L
+5=p             -------GRLVCT-VKAAA-AQ-QQDSASTQ------KAE---RE-VTKMVILMVLGF-L
+3==             -------GRLICK-VREAA-AQ-QQESATTQ------KAE---KE-VTRMVILMVLGF-M
+6==             -------GQLLIT-LKLAAKAQ-A-DSASTQ------KAE---RE-VTKMVVVMVLGFLV
+7==             -------RAL-----KAVA-AQ-QQESATTQ------KAE---RE-VSRMVVVMVGSFCV
+13==            --------NLLLT-LRAAA-AQ-Q-KEADTTQ-----RAE---RE-VTRMVIVMV-----
+30==            QKEVEECANLSRL-LKHERKNI----SIFKREQ----KAATTLGII-VGAFTVCWLPF--
+31=p            QKEVEECANLSRL-LKHERKNI----SIFKREQ----KAATTLGII-VGAFTVCWLPF--
+29==            QKEVEECANLSRL-LKHERKNI----SIFKREQ----KAATTLGII-VGAFTVCWLPF--
+32==            SG-SR-NWRLGV--ESKAGGA---L-CANGAVRQGDDGAALE-VIEVHRVG-NSKEHL--
+33=p            PG-SG-DWR-RC--AENRAVG---TPC-TNGAVRQGDDEATLEVIEVHRVG-NSKEHL--
+34==            NG-C---NSPDSTTEKKKRRAP-FKSYGCSPRPERKKNRAKKLPE--NANG-VNSNSS--
+35=p            NG-C---NSPDSTTEKKKRRAP-FKSYGCSPRPERKKNRAKKLPE--NANG-VNSNSS--
+36==            AL-V---AGGGS---GGIAAA----VVAVIGRPLPTISETTTTGF--TNVS-SNNTSP--
                                                                             
 
-14==            -------TAEIRIAKAAITICFLFFCSWTPYGVM-SLIGAF----GDKTLLTPGATMIPA
-15==            -------AAEIRIAKAAITICFLFFASWTPYGVM-SLIGAF----GDKTLLTPGATMIPA
-16==            -------TAEIRIAKAAITICFLFFVSWTPYGVM-SLIGAF----GDKSLLTQGATMIPA
-17==            -------TAEIRIAKAAITICFLFFVSWTPYGVM-SLIGAF----GDKSLLTPGATMIPA
-18==            --------AEIRIAKTALVNVSLWFICWTPYALI-SLKGVMGDTSG----ITPLVSTLPA
-19==            --------AEIRIAKTALVNVSLWFICWTPYAAI-TIQGLLGNAEG----ITPLLTTLPA
-20==            -------SAEGKLAKVALVTITLWFMAWTPYLVINCM-GLF-KFEG----LTPLNTIWGA
-21==            -------SAEGKLAKVALVTITLWFMAWTPYLVINCM-GLF-KFEG----LTPLNTIWGA
-22==            -------SAEGKLAKVALVTISLWFMAWTPYLVINCM-GLF-KFEG----LTPLNTIWGA
-23==            -------SAEGKLAKVALTTISLWFMAWTPYLVI-CYFGLF-KIDG----LTPLTTIWGA
-24==            -------SAENKLAKVALTTISLWFMAWTPYLII-CYFGLF-KIDG----LTPLTTIWGA
-25==            -------SAECKLAKVALMTISLWFMAWTPYLVI-NFSGIF-NLVK----ISPLFTIWGS
-26==            -------SAECRLAKVAMMTVGLWFMAWTPYLII-SWAGVF-S-SGTR--LTPLATIWGS
-27==            -------SAEMKLAKISMVIITQFMLSWSPYAII-ALLAQF----GPAEWVTPYAAELPV
-28==            -------NAEMRLAKISIVIVSQFLLSWSPYAVV-ALLAQF----GPLEWVTPYAAQLPV
-1==             --------AEKEVTRMVVLMVIGFLVCWVPYASVAFYIFTH---QGSD--FGATFMTLPA
-2==             --------AEKEVTRMVIIMVIFFLICWLPYASVAMYIFTH---QGSN--FGPIFMTLPA
-4=p             --------AEREVTKMVILMVFGFLIAWTPYATVAAWIFFN---KGAD--FSAKFMAIPA
-5=p             --------AEREVTKMVILMVLGFLVAWTPYATVAAWIFFN---KGAA--FSAQFMAIPA
-3==             --------AEKEVTRMVILMVLGFMLAWTPYAVVAFWIFTN---KGAD--FTATLMAVPA
-6==             --------AEREVTKMVVVMVLGFLVCWAPYASFSLWIVSH---RGEE--FDLRMATIPS
-7==             --------AEREVSRMVVVMVGSFCVCYVPYAAFAMYMVNN---RNHG--LDLRLVTIPS
-9==             --------AEKEVTRMVVVMVLAFCFCWGPYAFFACFAAAN---PGYP--FHPLMAALPA
-10==            --------AEKEVTRMVVVMIFAYCVCWGPYTFFACFAAAN---PGYA--FHPLMAALPA
-8=opsin_        --------AEKEVTRMVVVMVLAFC-----------------------------------
-11==            --------AEREVSRMVVVMIVAFCICWGPYASFVSFAAAN---PGYA--FHPLAAALPA
-12==            --------AEKEVSRMVVVMIVAYCFCWGPYTFFACFAAAN---PGYA--FHPLAAALPA
-13==            --------AEREVTRMVIVMVMAFLLCWLPYSTFALVVATH---KGII--IQPVLASLPS
-30==            RKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFI--CGTSCSCIPLWVERTCL
-31=p            RKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFI--CGTSCSCIPLWVERTCL
-29==            RKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFI--CGTSCSCIPLWVERTFL
-32==            KMAL---ARERKTVKTLGIIMGTFILCWLPFFIVALVLPF---CESSCH-MPTLLGAIIN
-33=p            KMAL---ARERKTVKTLGIIMGTFILCWLPFFIVALVLPF---CESSCH-MPALLGAIIN
-34==            KLEL---KRERKAARTLAIITGAFLICWLPFFIIALIGPF---VD--PEGIPPFARSFVL
-35=p            KLEL---KRERKAARTLAIITGAFLICWLPFFIIALIGPF---VD--PEGIPPFARSFVL
-36==            AADS---KRERKAAKTLAIITGAFVACWLPFFVLAILVPT---CD--CE-VSPVLTSLSL
-                         * .           :                                    
+14==            -----NVDKNKET----AEIRIAKAAI-TI----CFLFFC-----SWTP-YGV---MSLI
+15==            -----NVDKSKEA----AEIRIAKAAI-TI----CFLFFA-----SWTP-YGV---MSLI
+16==            -----NVDKSKET----AEIRIAKAAI-TI----CFLFFV-----SWTP-YGV---MSLI
+17==            -----NVDKSKET----AEIRIAKAAI-TI----CFLFFV-----SWTP-YGV---MSLI
+18==            -----NEA--DAQR---AEIRIAKTALVNV----SLWFI------CWTP-YALI---SLK
+19==            -----NEAE-TQ-R---AEIRIAKTALVNV----SLWFI------CWTP-YAAITIQGLL
+20==            ---SED-AE-K--S---AEGKLAKVALVTI----TLWF-------MAWTPYLVINCMGLF
+21==            ---SED-AE-K--S---AEGKLAKVALVTI----TLWF-------MAWTPYLVINCMGLF
+22==            ---SED-AD-K--S---AEGKLAKVALVTI----SLWF-------MAWTPYLVINCMGLF
+23==            ---SEDCD--K--S---AEGKLAKVALTTI----SLWF-------MAWTPYLVICYFGLF
+24==            ---SEDCD--K--S---AENKLAKVALTTI----SLWF-------MAWTPYLIICYFGLF
+25==            ---SENQN--T--S---AECKLAKVALMTI----SLWF-------MAWTPYLVINFSGIF
+26==            ---RANADQQKQ-S---AECRLAKVAMMTV----GLWF-------MAWTPYLIISWAGVF
+27==            TQFMLS-WSPYAIIALLAQFGPAEWVTPYAAELPVLFAKA-----SAIH-NPIVYSVSHP
+28==            L---LS-WSPYAVVALLAQFGPLEWVTPYAAQLPVMFAKA-----SAIH-NPMIYSVSHP
+9==             --FCFC-WGPYAFF---ACFAAANPGYPFHPLMAALPAFF---AKSAT-------IYNPV
+10==            --YCVC-WGPYTFF---ACFAAANPGYAFHPLMAALPAYF---AKSAT-------IYNPV
+8=opsin_        --FC--------------------------------------------------------
+11==            -AFCIC-WGPYASF---VSFAAANPGYAFHPLAAALPAYF---AKSAT-------IYNPV
+12==            -AYCFC-WGPYTFF---ACFAAANPGYAFHPLAAALPAYF---AKSAT-------IYNPI
+1==             CWVP-Y-A--SV-----AFYIFTHQGS----DFGATFMTL--PAFFA--K--SSALYNPV
+2==             CWLP-Y-A--SV-----AMYIFTHQGS----NFGPIFMTL--PAFFA--KTAS--IYNPI
+4=p             IAWTPY-AT-VA-----AWIFFNKGA-----DFS---AKF--MAIPAFFSK-SSALYNPV
+5=p             VAWTPY-AT-VA-----AWIFFNKGA-----AFS---AQF--MAIPAFFSK-TSALYNPV
+3==             LAWTPY-A--VV-----AFWIFTNKG-----A-DFT-ATL--MAVPAFFSK-SSSLYNPI
+6==             CWAP-Y-ASFSL-----WIVS-HRGEEF---DLRM--ATIPSCLSKA--ST-V---YNPV
+7==             CYVP-Y-A-AFA-----MYMV-NNRNH----GLDLRLVTIP-SFFS---KSAC--IYNPI
+13==            MAFLLC-WLPYSTF---ALVVATHKGIIIQPVLASLPSYF--S-KTAT-VY-NPIIYVFM
+30==            --FLLST------------ARPFICGT-------SC--SCIPLWVERTCLW-----LGYA
+31=p            --FLLST------------ARPFICGT-------SC--SCIPLWVERTCLW-----LGYA
+29==            --FLLST------------ARPFICGT-------SC--SCIPLWVERTFLW-----LGYA
+32==            --PLPSE------------AGP--TPCAPA----SFERKNER-NAEAK-RK-----MALA
+33=p            --PLPSES-----------GS---NSYAPA----CLERKNER-NAEAK-RK-----MALA
+34==            --SSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKIS-SN-DT-PY-----SRTR
+35=p            --SSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKIS-SN-DT-PY-----SRTR
+36==            --EKQS-------CANGLEADPPTTGY-GA----VAAAYYPSLVR-RK-PK-----EA-A
+                                                                            
 
-14==            CACKMVACIDPFVYAISHPRYRMELQKRCP--WLALNE--KAPESSAVASTSTTQEP-QQ
-15==            CTCKMVACIDPFVYAISHPRYRMELQKRCP--WLAISE--KAPESRAAISTSTTQEQ-QQ
-16==            CTCKLVACIDPFVYAISHPRYRLELQKRCP--WLGVNE--KSGEISSAQST-TTQEQ-QQ
-17==            CTCKLVACIEPFVYAISHPRYRMELQKRCP--WLGVNE--KSGEASSAQST-TTQEQTQQ
-18==            LLAKSCSCYNPFVYAISHPKYRLAITQHLP--WFCV-H--ETETKSND----DSQSN--S
-19==            LLAKSCSCYNPFVYAISHPKFRLAITQHLP--WFCV-H--EKDP--NDV--EENQSS--N
-20==            CFAKSAACYNPIVYGISHPKYRLALKEKCP---CCVFG--KVD----DGKSSDAQSQ--A
-21==            CFAKSAACYNPIVYGISHPKYRLALKEKCP---CCVFG--KVD----DGKSSDAQSQ--A
-22==            CFAKSAACYNPIVYGISHPKYRLALKEKCP---CCVFG--KVD----DGKSSEAQSQ--A
-23==            TFAKTSAVYNPIVYGISHPKYRIVLKEKCP---MCVFG--NTDEPKPDAPASDTE-----
-24==            TFAKTSAVYNPIVYGISHPNDRLVLKEKCP---MCVCG--TTDEPKPDAPPSDTE-----
-25==            LFAKANAVYNPIVYGISHPKYRAALFAKFPS-LACA------AEPSSDA-VSTTSGT--T
-26==            VFAKANSCYNPIVYGISHPRYKAALYQRFPS-LACGSG-----ESGSDV---KSEAS--A
-27==            LFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQF--DEKE-CEDANDAEEEVVASE
-28==            MFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQF--DDKE-TEDDKDAETEIPAGE
-1==             FFAKSSALYNPVIYILMNKQFRNCMITTLC----CGKNPLGDDE--SGASTSKTEVSSVS
-2==             FFAKTASIYNPIIYIMMNKQFRNCMLTSLC----CGKNPLGDDE--ASATASKTE-----
-4=p             FFSKSSALYNPVIYVLLNKQFRNCMLTTIF----CGKNPLGDDE-SSTVSTSKTEVSSVS
-5=p             FFSKTSALYNPVIYVLLNKQFRSCMLTTLF----CGKNPLGDEE-SSTVSTSKTEVSSVS
-3==             FFSKSSSLYNPIIYVLMNKQFRNCMITTIC----CGKNPFGDEDVSSTVSQSKTEVSSVS
-6==             CLSKASTVYNPVIYVLMNKQFRSCMMKMV-----CGKN-IEEDE--ASTSSQVTQVSSVA
-7==             FFSKSACIYNPIIYCFMNKQFQACIMKMV-----CGKA-MTDES--DTCSSQKTEVSTVS
-9==             FFAKSATIYNPVIYVFMNRQFRNCILQLF------G---KKVDDGSELSSASKTEVSSVS
-10==            YFAKSATIYNPVIYVFMNRQFRNCILQLF------G---KKVDDGSELSSASKTEVSSVS
+14==            G-AF-G--DKTLL----TPGA-T----MIPACAC--KM-VACIDPF--VYAI-S-HPRYR
+15==            G-AF-G--DKTLL----TPGA-T----MIPACTC--KM-VACIDPF--VYAI-S-HPRYR
+16==            G-AF-G--DKSLL----TQGA-T----MIPACTC--KL-VACIDPF--VYAI-S-HPRYR
+17==            G-AF-G--DKSLL----TPGA-T----MIPACTC--KL-VACIEPF--VYAI-S-HPRYR
+18==            GVMG-D---TSGI----TPLVSTLP-AL-LA-K---S--CSCYNPF--VYAI-S-HPKYR
+19==            GNAE-G--ITPLL----T----TLP-AL-LA-K---S--CSCYNPF--VYAI-S-HPKFR
+20==            KFE--G--LTPLN----TI---W---GACFA-K---SA-ACYNPI---VYGI-S-HPKYR
+21==            KFE--G--LTPLN----TI---W---GACFA-K---SA-ACYNPI---VYGI-S-HPKYR
+22==            KFE--G--LTPLN----TI---W---GACFA-K---SA-ACYNPI---VYGI-S-HPKYR
+23==            KID--G--LTPLT----TI---W---GATFA-KT--SA-VYNPI----VYGI-S-HPKYR
+24==            KID--G--LTPLT----TI---W---GATFA-KT--SA-VYNPI----VYGI-S-HPNDR
+25==            NLV--K--ISPLF----TI---W---GSLFA-KA--NA-VYNPI----VYGI-S-HPKYR
+26==            SSGT-R--LTPLA----TI---W---G--SV-FA--KA-NSCYNPI--VYGI-S-HPRYK
+27==            KFRE-AIQTTFPWLLTCCQFDEKECEDANDAEEE---V-VASERGGESRDAAQM-KEMMA
+28==            KFRE-AISQTFPWVLTCCQFDDKETEDDKDAETEI-PA-GESSDAAPSADAAQM-KEMMA
+9==             IYVF----MNRQF--RNCIL--QL-----FGKK--------VDDGSELSSA--S-KTEVS
+10==            IYVF----MNRQF--RNCIL--QL-----FGKK--------VDDGSELSSA--S-KTEVS
 8=opsin_        ------------------------------------------------------------
-11==            YFAKSATIYNPVIYVFMNRQFRNCIMQLF------G---KKVDDGSEASTTSRTEVSSVS
-12==            YFAKSATIYNPIIYVFMNRQFRNCILQLF------G---KKVDDGSEVST-SRTEVSSVS
-13==            YFSKTATVYNPIIYVFMNKQFQSCLLEMLC----CGYQPQRTGKASPGTPGPHADVTAAG
-30==            WLGYANSLINPFIYAFFNRDLRPTSRSLLQ----CQY-RNINRKLSAAGMHEALKLAERP
-31=p            WLGYANSLINPFIYAFFNRDLRTTYRSLLQ----CQY-RNINRKLSAAGMHEALKLAERP
-29==            WLGYANSLINPFIYAFFNRDLRTTYRSLLQ----CQY-RNINRKLSAAGMHEALKLAERP
-32==            WLGYSNSLLNPVIYAYFNKDFQNAFKKIIK----CKFCRQ--------------------
-33=p            WLGYSNSLLNPVIYAYFNKDFQNAFKKIIK----CKFCRR--------------------
-34==            WLGYFNSLLNPIIYTIFSPEFRSAFQKIL-----FGKYRRGHR-----------------
-35=p            WLGYFNSLLNPIIYTIFSPEFRSAFQKIL-----FGKYRRGHR-----------------
-36==            WLGYFNSTLNPVIYTVFSPEFRHAFQRLL-----CG--RRVRRRRAPQ------------
+11==            IYVF----MNRQF--RNCIM--QL-----FGKK--------VDDGSEASTT--S-RTEVS
+12==            IYVF----MNRQF--RNCIL--QL-----FGKK--------VDDGSEVST---S-RTEVS
+1==             IYIL----MNKQF--RNCMI--TT---LCCGKNPL-GDDE-SG-A---ST---S-KTEVS
+2==             IYIM----MNKQF--RNCML--TS---LCCGKNPL-GDDEASATA---SK-----TETSQ
+4=p             IYVL----LNKQF--RNCML--TT---IFCGKNPL-GD-DESSTV---ST---S-KTEVS
+5=p             IYVL----LNKQF--RSCML--TT---LFCGKNPL-GD-EESSTV---ST---S-KTEVS
+3==             IYVL----MNKQF--RNCMI--TT---ICCGKNPF-GDEDVSSTV---SQ---S-KTEVS
+6==             IYVL----MNKQF--RSCMM--K----MVCGKNIE-EDEA--STS---SQ---V-TQVSS
+7==             IYCF----MNKQFQ-ACIM----K---MVCGKA----MTDESDTC---SS---Q-KTEVS
+13==            NKQF-Q--SCLLE--MLCCG--YQP--QRTGKASP-GTPGPHADVTAAGL---R-NK-VM
+30==            NSLI-NPFIY--AFFNRDLR-PT------SRS------LLQCQYRNINRKLSAA---GMH
+31=p            NSLI-NPFIY--AFFNRDLR-TT------YRS------LLQCQYRNINRKLSAA---GMH
+29==            NSLI-NPFIY--AFFNRDLR-TT------YRS------LLQCQYRNINRKLSAA---GMH
+32==            RE---RKTVKTLGIIMGTFILCWLP-FFIVAL-----VLPFCESSCHMPTLLGA-IIN-W
+33=p            RE---RKTVKTLGIIMGTFILCWLP-FFIVAL-----VLPFCESSCHMPALLGA-IIN-W
+34==            EKLELKRERK--A--ARTLAIITGA-FLICWLPFFIIALIGPFVDPEGIPPFAR-SFVLW
+35=p            EKLELKRERK--A--ARTLAIITGA-FLICWLPFFIIALIGPFVDPEGIPPFAR-SFVLW
+36==            DS---KRERK--A--AKTLAIITGA-FVACWLPFFVLAILVPTCDCEVSP--VLTSLSLW
                                                                             
 
-14==            TTAA--------------------------------------------------------
-15==            TTAA--------------------------------------------------------
-16==            TTAA--------------------------------------------------------
-17==            TSAA--------------------------------------------------------
-18==            TVAQDKA-----------------------------------------------------
-19==            TQTQEKS-----------------------------------------------------
-20==            TASEAE-SKA--------------------------------------------------
-21==            TASEAE-SKA--------------------------------------------------
-22==            TTSEAE-SKA--------------------------------------------------
-23==            TTSEAD-SKA--------------------------------------------------
-24==            TTSEAE-SKD--------------------------------------------------
-25==            TVTDNEKSNA--------------------------------------------------
-26==            TTTMEEKPKIPEA-----------------------------------------------
-27==            R--GGESRDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGY--PPQGYPPQGAYPPPQGYPP
-28==            SSDAAPSADAAQMKEMMAMMQKMQQQQAAY----PPQGYAPPPQGYPPQG-YPP-QGYPP
-1==             T-SPVSPA----------------------------------------------------
-2==             T-SQVAPA----------------------------------------------------
-4=p             ------PA----------------------------------------------------
-5=p             ------PA----------------------------------------------------
-3==             S-SQVSPA----------------------------------------------------
-6==             ------PEK---------------------------------------------------
-7==             S-TQVGPN----------------------------------------------------
-9==             ---SVSPA----------------------------------------------------
-10==            ---SVSPA----------------------------------------------------
+14==            MELQKR--CPW-LAL--NE------K----APES-SAVA--STSTTQEPQ---QTT-AA-
+15==            MELQKR--CPW-LAI--SE------K----APES-RAAI--STSTTQEQQ---QTT-AA-
+16==            LELQKR--CPW-LGV--NE------KS---GEIS-SAQ---ST-TTQEQQ---QTT-AA-
+17==            MELQKR--CPW-LGV--NE------KS---GEAS-SAQ---ST-TTQEQT---QQTSAA-
+18==            LAITQHL--PWFCVHETET------KS---NDDSQSNS-------TV-AQ---DK---A-
+19==            LAITQHL--PWFCVHEKDP------ND---VEENQSSN-------TQTQE---KS-----
+20==            LALKEKCPCCV-FG---KV------DD---GKSS-DAQ---SQATASEAE---SK---A-
+21==            LALKEKCPCCV-FG---KV------DD---GKSS-DAQ---SQATASEAE---SK---A-
+22==            LALKEKCPCCV-FG---KV------DD---GKSS-EAQ---SQATTSEAE---SK---A-
+23==            IVLKEKCPMCV-FG---N-------TD---EPKP-DAPA-SDTETTSEAD---SK---A-
+24==            LVLKEKCPMCV-CG---T-------TD---EPKP-DAPP-SDTETTSEAE---SK---D-
+25==            AALFAKFPSLA-CAAEPSS------DA---VSTT-SGT---TTVTDNE-K---SN---A-
+26==            AALYQRFPSLA-CGSGESG------SD---VKSEASAT------TTMEEK---PKIPEA-
+27==            MMQK----MQAQQAA--YQPPPPPQGYPPQGYPPQGAYP-PPQGYPPQGYPPQGYPPQGY
+28==            MMQK----MQQQQAA--YPPQ----GY---APPPQG-YP-PQ-GYPPQGYPPQGYPPQGY
+9==             SVSSVS----P--A----------------------------------------------
+10==            SVSSVS----P--A----------------------------------------------
 8=opsin_        ------------------------------------------------------------
-11==            N-SSVAPA----------------------------------------------------
-12==            N-SSVSPA----------------------------------------------------
-13==            LRNKVMPAHPV-------------------------------------------------
-30==            ERSEFVLQNSDHCGKKGHDT----------------------------------------
-31=p            ERSEFVLQNSDHCGKKGHDT----------------------------------------
-29==            ERPEFVLQNADYCRKKGHDS----------------------------------------
-32==            ------------------------------------------------------------
-33=p            ------------------------------------------------------------
-34==            ------------------------------------------------------------
-35=p            ------------------------------------------------------------
-36==            ------------------------------------------------------------
+11==            SVSNSS----V--APA--------------------------------------------
+12==            SVSNSS----VSPA----------------------------------------------
+1==             SVSTSP----VSPA----------------------------------------------
+2==             VAP-------A-------------------------------------------------
+4=p             SVSP------A-------------------------------------------------
+5=p             SVSP------A-------------------------------------------------
+3==             SVSSSQ----VSPA----------------------------------------------
+6==             VAPEK-------------------------------------------------------
+7==             TVSSTQ----VGPN----------------------------------------------
+13==            PAHP------V-------------------------------------------------
+30==            EALKLAE---RPERSEFVLQ-N---SDH-----CGK----KGHD-T--------------
+31=p            EALKLAE---RPERSEFVLQ-N---SDH-----CGK----KGHD-T--------------
+29==            EALKLAE---RPERPEFVLQ-N---ADY-----CRK----KGHDS---------------
+32==            LG-YSN----SLLN--PVIYAY--FNKDFQNAF-KKIIKCKFCRQ---------------
+33=p            LG-YSN----SLLN--PVIYAY--FNKDFQNAF-KKIIKCKFCRR---------------
+34==            LG-YFN----SLLNPIIYTIFSPEFRSAFQKILFGK-YR-RGHR----------------
+35=p            LG-YFN----SLLNPIIYTIFSPEFRSAFQKILFGK-YR-RGHR----------------
+36==            LG-YFN----STLNPVIYTVFSPEFRHAFQRLLCGRRVR-RRRAPQ--------------
                                                                             
 
-14==            ----------------------------------------
-15==            ----------------------------------------
-16==            ----------------------------------------
-17==            ----------------------------------------
-18==            ----------------------------------------
-19==            ----------------------------------------
-20==            ----------------------------------------
-21==            ----------------------------------------
-22==            ----------------------------------------
-23==            ----------------------------------------
-24==            ----------------------------------------
-25==            ----------------------------------------
-26==            ----------------------------------------
-27==            QGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQA
-28==            QGYPPQGYPP---PPQGAPPQ-GAPPAAPPQGVDNQAYQA
-1==             ----------------------------------------
-2==             ----------------------------------------
-4=p             ----------------------------------------
-5=p             ----------------------------------------
-3==             ----------------------------------------
-6==             ----------------------------------------
-7==             ----------------------------------------
-9==             ----------------------------------------
-10==            ----------------------------------------
-8=opsin_        ----------------------------------------
-11==            ----------------------------------------
-12==            ----------------------------------------
-13==            ----------------------------------------
-30==            ----------------------------------------
-31=p            ----------------------------------------
-29==            ----------------------------------------
-32==            ----------------------------------------
-33=p            ----------------------------------------
-34==            ----------------------------------------
-35=p            ----------------------------------------
-36==            ----------------------------------------
-                                                        
+14==            -----------------------------
+15==            -----------------------------
+16==            -----------------------------
+17==            -----------------------------
+18==            -----------------------------
+19==            -----------------------------
+20==            -----------------------------
+21==            -----------------------------
+22==            -----------------------------
+23==            -----------------------------
+24==            -----------------------------
+25==            -----------------------------
+26==            -----------------------------
+27==            PPQ--GAPPQVEAPQGAPPQGVDNQAYQA
+28==            PPPPQGAPPQG-APPAAPPQGVDNQAYQA
+9==             -----------------------------
+10==            -----------------------------
+8=opsin_        -----------------------------
+11==            -----------------------------
+12==            -----------------------------
+1==             -----------------------------
+2==             -----------------------------
+4=p             -----------------------------
+5=p             -----------------------------
+3==             -----------------------------
+6==             -----------------------------
+7==             -----------------------------
+13==            -----------------------------
+30==            -----------------------------
+31=p            -----------------------------
+29==            -----------------------------
+32==            -----------------------------
+33=p            -----------------------------
+34==            -----------------------------
+35=p            -----------------------------
+36==            -----------------------------
+                                             
diff --git a/tools/clustalw/test-data/rgClustal_testout03.dnd b/tools/clustalw/test-data/rgClustal_testout03.dnd
new file mode 100644
index 000000000..1b1dd71db
--- /dev/null
+++ b/tools/clustalw/test-data/rgClustal_testout03.dnd
@@ -0,0 +1,103 @@
+(
+(
+(
+(
+(
+1==:0.10508,
+2==:0.11044)
+:0.03328,
+(
+3==:0.10212,
+(
+4=p:0.03956,
+5=p:0.04640)
+:0.07123)
+:0.03527)
+:0.12883,
+6==:0.25691)
+:0.03351,
+7==:0.25261)
+:0.01354,
+(
+(
+(
+8=opsin_:0.00232,
+(
+9==:0.01369,
+10==:0.02751)
+:0.00485)
+:0.08347,
+(
+11==:0.07845,
+12==:0.09558)
+:0.02853)
+:0.20130,
+(
+(
+(
+(
+(
+14==:0.03776,
+15==:0.05125)
+:0.12161,
+(
+16==:0.05295,
+17==:0.05551)
+:0.09431)
+:0.20019,
+(
+(
+18==:0.12284,
+19==:0.12385)
+:0.20199,
+(
+(
+(
+(
+(
+20==:0.02082,
+21==:-0.01799)
+:0.02913,
+22==:0.01073)
+:0.15908,
+(
+23==:0.03644,
+24==:0.05280)
+:0.11950)
+:0.05528,
+25==:0.22127)
+:0.02122,
+26==:0.23721)
+:0.07307)
+:0.02400)
+:0.03308,
+(
+27==:0.14728,
+28==:0.12727)
+:0.26343)
+:0.04564,
+(
+(
+29==:0.02761,
+(
+30==:0.00213,
+31=p:0.00282)
+:0.02437)
+:0.38262,
+(
+(
+32==:0.04954,
+33=p:0.05235)
+:0.33117,
+(
+(
+34==:0.00000,
+35=p:0.00000)
+:0.33155,
+36==:0.33885)
+:0.04452)
+:0.02854)
+:0.07289)
+:0.12569)
+:0.01983,
+13==:0.31664);

From 640e6104faa27a29731c57d75c0a653afd8853b4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
 <gallardo@informatik.uni-freiburg.de>
Date: Thu, 15 Sep 2022 13:47:29 +0200
Subject: [PATCH 4/4] Fix test

---
 tools/clustalw/macros.xml                     |   2 +-
 tools/clustalw/rgClustalw.xml                 |   2 +-
 .../test-data/rgClustal_testout03.aln         | 832 +++++++++---------
 .../test-data/rgClustal_testout03.dnd         | 134 +--
 4 files changed, 504 insertions(+), 466 deletions(-)

diff --git a/tools/clustalw/macros.xml b/tools/clustalw/macros.xml
index 7adbb9801..0085346ff 100644
--- a/tools/clustalw/macros.xml
+++ b/tools/clustalw/macros.xml
@@ -1,4 +1,4 @@
-    <macros>
+<macros>
     <token name="@TOOL_VERSION@">2.1</token>
     <token name="@VERSION_SUFFIX@">1</token>
     <xml name="requirements">
diff --git a/tools/clustalw/rgClustalw.xml b/tools/clustalw/rgClustalw.xml
index 67b49914a..a242b23f7 100644
--- a/tools/clustalw/rgClustalw.xml
+++ b/tools/clustalw/rgClustalw.xml
@@ -171,7 +171,7 @@ $tree_calculation.TOSSGAPS
                 <param name="TOSSGAPS" value="false"/>
             </section>
             <conditional name="type_conditional">
-                <param name="selector" value="PROTEIN"/>
+                <param name="dnarna" value="PROTEIN"/>
                 <section name="multiple_alignments">
                     <param name="MATRIX" value="BLOSUM"/>
                     <param name="GAPOPEN" value="3"/>
diff --git a/tools/clustalw/test-data/rgClustal_testout03.aln b/tools/clustalw/test-data/rgClustal_testout03.aln
index e238ca487..151e10081 100644
--- a/tools/clustalw/test-data/rgClustal_testout03.aln
+++ b/tools/clustalw/test-data/rgClustal_testout03.aln
@@ -1,420 +1,458 @@
 CLUSTAL 2.1 multiple sequence alignment
 
 
-14==            -------------------------------------MESGNVS-SSLFGN-VSTALRPE
-15==            -----------------------------------MEYHNVSSVLGN--VS-SVLRPD--
-16==            ----------------------------------MEPLCNASEPPLRPEAR-SS------
-17==            ----------------------------------MDALCNASEPPLRPEAR-MS------
-18==            ----------------------------------------MTN-ATGPQMAYYG-AASMD
-19==            ---------------------------------------MANV--TGPQMAFYGSGA-AT
-20==            ---------------------------MESFA------VAAAQLGPHF-AP-LSN-GS--
-21==            ---------------------------MESFA------VAAAQLGPHF-AP-LSN-GS--
-22==            ---------------------------MDSFA------AVATQLGPQF-AA-PSN-GS--
-23==            ---------------------------MERSHLPETPFDLAHS-GPRFQAQ-SSG-NG--
-24==            ---------------------------MERSLLPEPPLAMALL-GPRFEAQ-TGG-NR--
-25==            --------------------------------------MIAVS-GPSYEAFSYGGQARF-
-26==            ---------------------------------------MANQLSYSSLGWPYQPNAS--
-27==            ----------------------------------------------------MVE-----
-28==            ----------------------------------------------------MG------
-9==             ---------------------------------------MAQQWSLQRLAGRHPQDSYE-
-10==            ---------------------------------------MAQQWSLQRLAGRHPQDSYE-
+14==            ------------------------------------MESGNV-SSSLFGNVSTA-LRPEA
+15==            ------------------------------------MEYHNV-SSVL-GNVSSV-LRPDA
+16==            ------------------------------------ME-------PL-CNASEPPLRPEA
+17==            ------------------------------------MD-------AL-CNASEPPLRPEA
+18==            -----------------------------------------------MTNATG----PQM
+19==            -----------------------------------------------MANVTG----PQM
+20==            ------------------------------------ME-SFA----VAAAQLG----PH-
+21==            ------------------------------------ME-SFA----VAAAQLG----PH-
+22==            ------------------------------------MD-SFA----AVATQLG----PQ-
+23==            ------------------------------------MERSHLPETPFDLAHSG----PR-
+24==            ------------------------------------MERSLLPEPPLAMALLG----PR-
+25==            -----------------------------------------------MIAVSG----PS-
+26==            ------------------------------------------MANQLSYSSLGW---P--
+27==            ------------------------------------------------------------
+28==            ------------------------------------------------------------
+1==             -----------------------------------------------------MNGT-E-
+2==             -----------------------------------------------------MNGT-E-
+4=p             -----------------------------------------------------MNGT-E-
+5=p             -----------------------------------------------------MNGT-E-
+3==             -----------------------------------------------------MNGT-E-
+6==             -----------------------------------------------------MKQVPEF
+7==             -----------------------------------------------------MRKMSE-
+9==             -----------------------------------------MAQQWSLQRLAGRHPQDSY
+10==            -----------------------------------------MAQQWSLQRLAGRHPQDSY
 8=opsin_        ------------------------------------------------------------
-11==            -----------------------------------MTEAWNV-A---VFAARR--SRDD-
-12==            --------------------------------------MAAWEA---AFAARR--RHEE-
-1==             ----------------------------------------MN--G---TEGDNFYVPFS-
-2==             ----------------------------------------MN--G---TEGPNFYVPFS-
-4=p             ----------------------------------------MN--G---TEGKNFYVPMS-
-5=p             ----------------------------------------MN--G---TEGNNFYVPLS-
-3==             ----------------------------------------MN--G---TEGINFYVPMS-
-6==             ----------------------------------------MKQ-VPEFHEDFYIPIPLD-
-7==             ---------------------------------------MRKM-S---EEEFYLFKNIS-
-13==            ----------------------------------------MS--S-------NSSQAPP-
-30==            --------------------------------------------MPHLLS-GFLE-----
-31=p            --------------------------------------------MPHLLS-GFLE-----
-29==            -------MMDVNSSGRPDLYGHLRSFLLPEVGRGLPDLSPDGGADPVAGSWAPHLLSE--
-32==            -------------------------------------------------MDVL-------
-33=p            -------------------------------------------------MDVF-------
-34==            MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGL---VTSDFNDSYGLTGQFI
-35=p            MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGL---VTSDFNDSYGLTGQFI
-36==            --------------------ME-GAEGQEELDWEALYL-RLPLQNCSWNSTGWEPN----
+11==            -----------------------------------------MTEAWNVAVFAARRSRDD-
+12==            -----------------------------------------MA-AWEAA-FAARRRHEE-
+13==            ------------------------------------------------------------
+30==            ------------------------------------------------------------
+31=p            ------------------------------------------------------------
+29==            ---------------------MMDVNSSGRPDLYGHLRSFLLPEVGRGLPDLSPDGGADP
+32==            -----------------------------------------------MDVL-SPGQ-GNN
+33=p            -----------------------------------------------MDVF-SFGQ-GNN
+34==            MANFTFGDLALDVARM-GGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFING
+35=p            MANFTFGDLALDVARM-GGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFING
+36==            ---------------MEGAEGQEELDWEALYLRLP-LQ---------NCSWNSTGWEPNW
                                                                             
 
-14==            ARL-----SAETRLLGWNVPPEELRHI-PEHWLTYPEPPESMNYLLG--TLYIF-----F
-15==            ARL-----SAESRLLGWNVPPDELRHI-PEHWLIYPEPPESMNYLLG--TLYIF-----F
-16==            -GN-----GDLQFL-GWNVPPDQIQYI-PEHWLTQLEPPASMHYMLGVFYIFLF------
-17==            -SG-----SDELQFLGWNVPPDQIQYI-PEHWLTQLEPPASMHYMLGVFYIFLF------
-18==            FGYPEGV-SIV-DF--VRPEIKPYVHQ-HWYNYPP-VNP-MWHYLLGV---IYL-----F
-19==            FGYPEGMTVADFVP--DR---VKHMVL-DHWYNYPPVNP-MWHYLLGV---VYL-----F
-20==            -VV----DKVTPD---MA---HLISP---YWNQFPAMDPIWAKILTA--Y-MI------M
-21==            -VV----DKVTPD---MA---HLISP---YWNQFPAMDPIWAKILTA--Y-MI------M
-22==            -VV----DKVTPD---MA---HLISP---YWDQFPAMDPIWAKILTA--Y-MI------I
-23==            -SV---LDNVLPD---MA---HLVNP---YWSRFAPMDP-MMSKILGLFTLAI------M
-24==            -SV---LDNVLPD---MA---PLVNP---HWSRFAPMDP-TMSKILGLFTLVI------L
-25==            -NN---QTVVDKVP-PDML--HLIDA---NWYQYPPLNP-MWHGILGF---VIG-----M
-26==            -VV---DTMPKEML--YM-----IHE---HWYAFPPMNP-LWYSILGV---AMI-----I
-27==            -STTL---VNQTWW--YNPT-V-DIHP-HWAKFDPIPDAVYYSV--GIFIGVV-------
-28==            -RDLR---DNETWW--YNP--SIVVHP-HWREFDQVPDAVYYSL--GIFIGIC-------
-9==             -DSTQS--SIFTYTNSNS---TRGPFEGPNYHIAPRWVYHLTSVW-MI-----------F
-10==            -DSTQS--SIFTYTNSNS---TRGPFEGPNYHIAPRWVYHLTSVW-MI-----------F
+14==            RLSA---ETRLLGWN------VPPEELRH-IPEHWLTYPE-PPES--MNYLLGT---LYI
+15==            RLSA---ESRLLGWN------VPPDELRH-IPEHWLIYPE-PPES--MNYLLGT---LYI
+16==            R-SSGNGDLQFLGWN------VPPDQIQY-IPEHWLTQLE-PPAS--MHYMLGV---FYI
+17==            RMSSGSDELQFLGWN------VPPDQIQY-IPEHWLTQLE-PPAS--MHYMLGV---FYI
+18==            AYYGAASMDFGYPEGVSIVDFVRPE-IKPYVHQHWYNY---PPVNPMWHYLLGV---IYL
+19==            AFYGSGAATFGYPEGMTVADFV-PDRVKHMVLDHWYNY---PPVNPMWHYLLGV---VYL
+20==            -F-A-PL------SNGSVVDKVTPD-MAHLISPYWNQF---PAMDPIWAKILTA---YMI
+21==            -F-A-PL------SNGSVVDKVTPD-MAHLISPYWNQF---PAMDPIWAKILTA---YMI
+22==            -F-AAP-------SNGSVVDKVTPD-MAHLISPYWDQF---PAMDPIWAKILTA---YMI
+23==            -FQAQSS------GNGSVLDNVLPD-MAHLVNPYWSRFA--P-MDPMMSKILGL---FTL
+24==            -FEAQTG------GNRSVLDNVLPD-MAPLVNPHWSRFA--P-MDPTMSKILGL---FTL
+25==            -YEAFSYGGQARFNNQTVVDKVPPD-MLHLIDANWYQY---PPLNPMWHGILG----FVI
+26==            -Y--QP--------NASVVDTMPKE-MLYMIHEHWYAF---PPMNPLWYSILGV---AMI
+27==            -----MVESTTLV-NQTW--WYNPTVDIH---PHWAKFDPIP--DAVYYS-VG----IFI
+28==            -----M--GRDLRDNETW--WYNPSIVVH---PHWREFDQVP--DAVYYS-LG----IFI
+1==             GDNFYV-PF----SNKTGLARSPYE------YPQY-YLA------EPWKYSALA---AYM
+2==             GPNFYV-PF----SNITGVVRSPFE------QPQY-YLA------EPWQFSMLA---AYM
+4=p             GKNFYV-PM----SNRTGLVRSPFE------YPQY-YLA------EPWQFKILA---LYL
+5=p             GNNFYV-PL----SNRTGLVRSPFE------YPQY-YLA------EPWQFKLLA---VYM
+3==             GINFYV-PM----SNKTGVVRSPFE------YPQY-YLA------EPWKYRLVC---CYI
+6==             HEDFYI-PIPLDINNLSAY--SPFL------VPQD-HLG------NQGIFMAMS---VFM
+7==             -EEFYLF------KNISSV--GPWD------GPQY-HIA------PVWAFYLQA---AFM
+9==             EDSTQSSIFTYTNSNST---RGPFE------GPNY-HIA------PRWVYHLTS---VWM
+10==            EDSTQSSIFTYTNSNST---RGPFE------GPNY-HIA------PRWVYHLTS---VWM
 8=opsin_        ------------------------------------------------------------
-11==            -DDTTRG-SVFTYTNTNN---TRGPFEGPNYHIAPRWVYNL-VSFFMI-----------I
-12==            -EDTTRD-SVFTYTNSNN---TRGPFEGPNYHIAPRWVYNLTSVW-MI-----------F
-1==             -NKT-GLARSPYEYPQY----YLAE----PWKYSALAA---YMFFLI------------L
-2==             -NIT-GVVRSPFEQPQY----YLAE----PWQFSMLAA---YMFLLI------------V
-4=p             -NRT-GLVRSPFEYPQY----YLAE----PWQFKILAL---YLFFLM------------S
-5=p             -NRT-GLVRSPFEYPQY----YLAE----PWQFKLLAV---YMFFLI------------C
-3==             -NKT-GVVRSPFEYPQY----YLAE----PWK-YRLVC---CYIFFLI-----------S
-6==             -INNLSAYSPFL-VPQD----HLG------NQGIFMAM---SVFMFFI-----------F
-7==             -SV--GPWDGPQ----Y----HIAP----VWAFYLQAAFMGTVFLIGF-----------P
-13==            -NGTPGPFDGPQ----WP---YQAPQ---STY-VGVAVLMGTVVACAS-----------V
-30==            --VTASP-APTWDAPPDNVSGC-GEQI--NYGRVEKVV---IGSILTLITLL-------T
-31=p            --VTASP-APTWDAPPDNVSGC-GEQI--NYGRVEKVV---IGSILTLITLL-------T
-29==            --VTASP-APTWDAPPDNASGC-GEQI--NYGRVEKVV---IGSILTLITLL-------T
-32==            --SPGQ--GNNTT-SPPAPFETGGN----TTGI--SDV---TVS-YQVITSLLLGTLIFC
-33=p            --SFGQ--GNNTTASQEPFG-TGGN----VTSI--SDV---TFS-YQVITSLLLGTLIFC
-34==            NGSHSS--RSRDNASANDTSAT-NM----TDDR--YWSLTVYSHEHLVLTSVILGLFVLC
-35=p            NGSHSS--RSRDNASANDTSAT-NM----TDDR--YWSLTVYSHEHLVLTSVILGLFVLC
-36==            WNVTVV--PNTTWWQASAPFDTPAA----LVRAAAKAV--VLGLLILA-TVV--------
+11==            DDTTRGSVFTYTNTNNT---RGPFE------GPNY-HIA------PRWVYNLVS---FFM
+12==            EDTTRDSVFTYTNSNNT---RGPFE------GPNY-HIA------PRWVYNLTS---VWM
+13==            ----MSSNSSQAPPNGT---PGPFD------GPQWPYQA------PQSTYVGVA---VLM
+30==            -----MPHLLSGFLEVTASPAPT----WDAPPDNVSGCGEQINYGRVEKVVIGS----IL
+31=p            -----MPHLLSGFLEVTASPAPT----WDAPPDNVSGCGEQINYGRVEKVVIGS----IL
+29==            VAGSWAPHLLS---EVTASPAPT----WDAPPDNASGCGEQINYGRVEKVVIGS----IL
+32==            TTSPPAPFETGG--NTTGISDVTVS-YQ----------------------VITS---LLL
+33=p            TTASQEPFGTGG--NVTSISDVTFS-YQ----------------------VITS---LLL
+34==            SHSSRSRDNASA--NDTSATNMTDDRYW------------SLTVYSHEHLVLTS---VIL
+35=p            SHSSRSRDNASA--NDTSATNMTDDRYW------------SLTVYSHEHLVLTS---VIL
+36==            --------------NVTVVPNTT---WWQA----------SAPFDTPAALVRAAAKAVVL
                                                                             
 
-14==            TL--M--SMLGNGLVIWV--FSAA--KSLRTPSNILVINLAFCDFMMM-VKTPIFIYNSF
-15==            TV--I--SMIGNGLVMWV--FSAA--KSLRTPSNILVINLAFCDFMMM-IKTPIFIYNSF
-16==            CA--STVGN-GMVIWIFS--TS----KSLRTPSNMFVLNLAVFDLIMC-LKAPIF--NSF
-17==            FA--STLGN-GMVIWIFS--TS----KSLRTPSNMFVLNLAVFDLIMC-LKAPIFIYNSF
-18==            LGT-V-SIF-GNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTNV-PFFTY---NCF
-19==            LG--VISIA-GNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTNF-PPFCY---NCF
-20==            IGMISWCGN-GVVIYIFATTKSLR--TPANLLVINLAISDF---GIMI-TNTPMMGINLY
-21==            IGMISWCGN-GVVIYIFATTKSLR--TPANLLVINLAISDF---GIMI-TNTPMMGINLY
-22==            IGMISWCGN-GVVIYIFATTKSLR--TPANLLVINLAISDF---GIMI-TNTPMMGINLY
-23==            IIS-C-CGN-GVVVYIFGGTKSLR--TPANLLVLNLAFSDFCMMA-SQ--SP-VMIINFY
-24==            IIS-C-CGN-GVVVYIFGGTKSLR--TPANLLVLNLAFSDFCMMA-SQ--SP-VMIINFY
-25==            LGFVSAMGN-GMVVYIFLSTKSLR--TPSNLFVINLAISNFLMMFCM---SPPMVI-NCY
-26==            LGIICVLGN-GMVIYLMMTTKSLR--TPTNLLVVNLAFSDFCMMAFM---MPTM---TSN
-27==            -GIIGILGN-GVVIYLFSKTKSLQ--TPANMFIINLA-MS-DLSFSAI-NGFPL---KTI
-28==            -GIIGCGGN-GIVIYLFTKTKSLQ--TPANMFIINLAFSDFTFSLVN--GFPLM---TIS
-9==             VVIASVFTN-GLVLAATMKFKKLR--HPLNWILVNLAVADLAETVIASTIS----V-VNQ
-10==            VVTASVFTN-GLVLAATMKFKKLR--HPLNWILVNLAVADLAETVIASTIS----I-VNQ
-8=opsin_        ---------------------------------------DLAETVIASTIS----I-VNQ
-11==            VVIASCFTN-GLVLVATAKFKKLR--HPLNWILVNLAFVDLVETLVASTIS----V-FNQ
-12==            VVAASVFTN-GLVLVATWKFKKLR--HPLNWILVNLAVADLGETVIASTIS----V-INQ
-1==             VGFPV---N-FLTLFVTVQHKKLR--TPLNYILLNLAM-A--NLFMVL-FGFTVTM-YTS
-2==             LGFPI---N-FLTLYVTVQHKKLR--TPLNYILLNLAV-A--DLFMVF-GGFTTTL-YTS
-4=p             MGLPI---N-GLTLVVTAQHKKLR--QPLNFILVNLAV-A--GTIMVC-FGFTVTF-YTA
-5=p             LGLPI---N-GLTLICTAQHKKLR--QPLNFILVNLAV-A--GAIMVC-FGFTVTF-YTA
-3==             TGLPI---N-LLTLLVTFKHKKLR--QPLNYILVNLAV-A--DLFMAC-FGFTVTF-YTA
-6==             IGGASI--N-ILTILCTIQFKKLR--SHLNYILVNL-SIA--NLFVAIFGSPLSFY-SFF
-7==             LNAMVL--V-A-----TLRYKKLR--QPLNYILVN-VSFG--GFLLCIFSVFPVFVASC-
-13==            VNGLVI--V-V---SIC--YKKLR--SPLNYILVNLAVADLLVTLCGS-SV----SLSNN
-30==            ---IAGN-CLVVISVSFVK--KLRQ--PSNYLIVSLALADLSVAVAVMPFV-----SVTD
-31=p            ---IAGN-CLVVISVSFVK--KLRQ--PSNYLIVSLALADLSVAVAVMPFV-----SVTD
-29==            ---IAGN-CLVVISVCFVK--KLRQ--PSNYLIVSLALADLSVAVAVMPFV-----SVTD
-32==            AVLGNAC-VVAA-IALERSLQNVA-----NYLIGSLAV-TDLMVSVLVLPMA----ALYQ
-33=p            AVLGNAC-VVAA-IALERSLQNVA-----NYLIGSLAV-TDLMVSVLVLPMA----ALYQ
-34==            -CIIGNCFVIAA-VMLERSLHNVA-----NYLILSLAVADLMVAVLVMPLSV----VSEI
-35=p            -CIIGNCFVIAA-VMLERSLHNVA-----NYLILSLAVADLMVAVLVMPLSV----VSEI
-36==            ----GNVFVIAA-ILLERHLRSAA-----NNLILSLAVADLLVACLVMPLGA----VYEV
-                                                                            
+14==            -FFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDF-MMMVK-TPIFIYNSFHQGY
+15==            -FFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDF-MMMIK-TPIFIYNSFHQGY
+16==            -FLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDL-IMCLK-APIF--NSFHRGF
+17==            -FLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDL-IMCLK-APIFIYNSFHRGF
+18==            -FLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTN-VPFFTYNCFSGG-
+19==            -FLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTN-FPPFCYNCFSGG-
+20==            -MIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLYFE--
+21==            -MIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLYFE--
+22==            -IIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLYFE--
+23==            -AIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVMIINFYYE--
+24==            -VILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVMIINFYYE--
+25==            GMLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCM-SPPMVINCYYE--
+26==            -ILGIICVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFM-MPTMTSNCFAE--
+27==            GVVGIIGILGNGVVIYLFSKTKSLQTPANMFIINLAMSDLSFSAINGFPLKTISAFMK--
+28==            GICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLVNGFPLMTISCFLK--
+1==             FFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFG-FTVTMYTSMNGY-
+2==             FLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGG-FTTTLYTSLHGY-
+4=p             FFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNLAVAGTIMVCFG-FTVTFYTAINGY-
+5=p             FFLICLGLPINGLTLICTAQHKKLRQPLNFILVNLAVAGAIMVCFG-FTVTFYTAINGY-
+3==             FFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFG-FTVTFYTAWNGY-
+6==             FFIFIGGASINILTILCTIQFKKLRSHLNYILVNLSIANLFVAIFG-SPLSFYSFFNRY-
+7==             GTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIFSVFPV-FVASCNGY-
+9==             IFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STISVVNQVYGY-
+10==            IFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STISIVNQVSGY-
+8=opsin_        --------------------------------------DLAETVIA-STISIVNQVSGY-
+11==            IIVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVA-STISVFNQIFGY-
+12==            IFVVAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIA-STISVINQISGY-
+13==            GTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLCG-SSVSLSNNINGF-
+30==            TLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDLIGG-
+31=p            TLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDLIGG-
+29==            TLITLLTIAGNCLVVISVCFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDLIGG-
+32==            GTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAALYQVLN--
+33=p            GTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAALYQVLN--
+34==            GLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVSEISK--
+35=p            GLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVSEISK--
+36==            GLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLV-MPLGAVYEVVQ--
+                                                      .         .           
 
-14==            HQG--YA---LG---HLGC-QIFGI--IGSYTGIAA--GATN-AFIA--YDRFNVITRPM
-15==            HQG--YA---LG---HLGC-QIFGV--IGSYTGIAA--GATN-AFIA--YDRYNVITRPM
-16==            HRG--FAIYLGN---TW-C-QIFAS--IGSYSGIGA--GMTN-AAIG--YDRYNVITKPM
-17==            HRG--FA--LGN---TW-C-QIFAS--IGSYSGIGA--GMTN-AAIG--YDRYNVITKPM
-18==            SGG-VWMF---SPQYCEIY-ACLGA--ITGVCSI-WLLCMISFD--R--YNIICN--GFN
-19==            SGG-RWMF---SGTYCEIY-AALGA--ITGVCSI-WTLCMISFD--R--YNIICN--GFN
-20==            FE---TWV--LGPMMCDIY-AGLGS--AFGCSSI-W--SMCMISLDR--YQVIVK--G-M
-21==            FE---TWV--LGPMMCDIY-AGLGS--AFGCSSI-W--SMCMISLDR--YQVIVK--G-M
-22==            FE---TWV--LGPMMCDIY-AGLGS--AFGCSSI-W--SMCMISLDR--YQVIVK--G-M
-23==            YE---TWV--LGPLWCDIY-AGCGS--LFGCVSI-W--SMCMIAFDR--YNVIVK--G-I
-24==            YE---TWV--LGPLWCDIY-AACGS--LFGCVSI-W--SMCMIAFDR--YNVIVK--G-I
-25==            YE---TWV--LGPLFCQIY-AMLGS--LFGCGSI-W--TMTMIAFDR--YNVIVK--GLS
-26==            CFA-ETWI--LGPFMCEVY-GMAGS--LFGCASI-W--SMVMITLDR--YNVIVR--G-M
-27==            SAFMKKWI--FGKVACQLY-GLLGG--IFGFMSI-NTMAMISID--R--YNVIGRPMA-A
-28==            CFL-KKWI--FGFAACKVY-GFIGG--IFGFMSI-MTMAMISID--R--YNVIGRPMA-A
-9==             VYG--YFV--LGHPMCV---L-EG--YTVSLC-GIT--GLWSLAIIS--WERWMVVCKPF
-10==            VSG--YFV--LGHPMCV---L-EG--YTVSLC-GIT--GLWSLAIIS--WERWLVVCKPF
-8=opsin_        VSG--YFV--LGHPMCV---L-EG--YTVSLC-GIT--GLWSLAIIS--WERWLVVCKPF
-11==            IFG--YFI--LGHPLCVIE-G-YV--V-SS-C-GIT--GLWSLAIIS--WERWFVVCKPF
-12==            ISG--YFI--LGHPMCV---V-EG--YTVSAC-GIT--ALWSLAIIS--WERWFVVCKPF
-1==             MNG--YFV--FGPTMCSIE-GFFA--TLGGEV-ALW--SLVVLAIER--Y---IVICKPM
-2==             LHG--YFV--FGPTGCNLE-GFFA--TLGGEI-GLW--SLVVLAIER--Y---VVVCKPM
-4=p             ING--YFV--LGPTGCAVE-GFMA--TLGGEV-ALW--SLVVLAIER--Y---IVVCKPM
-5=p             ING--YFA--LGPTGCAVE-GFMA--TLGGEV-ALW--SLVVLAIER--Y---IVVCKPM
-3==             WNG--YFV--FGPVGCAVE-GFFA--TLGGQV-ALW--SLVVLAIER--Y---IVVCKPM
-6==             -NR--YFI--FGATACKIE-GFLA--TLGGMV-GLW--SLAVVAFER--W---LVICKPL
-7==             -NG--YFV--FGRHVCALE-GFLG--TVAGLVTG-W--SLAFLAFER--Y---IVICKPF
-13==            ING--FFV--FGRRMCELE-GFMVSLT--GIV-GLW--SLAILALER--Y---VVVCKPL
-30==            LIG-GKWIFGHFFCNVFI--AMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCM
-31=p            LIG-GKWIFGHFFCNVFI--AMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCM
-29==            LIG-GKWIFGHFFCNVFI--AMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCM
-32==            VLN-KWT---LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPR-R
-33=p            VLN-KWT---LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPR-R
-34==            S-K-VWFLHSEV-CDMWIS-V-DVLCCTASILHLVAIAMDRYWAVTSI-DYIRRR--S-A
-35=p            S-K-VWFLHSEV-CDMWIS-V-DVLCCTASILHLVAIAMDRYWAVTSI-DYIRRR--S-A
-36==            VQR-WTL--GPELCDMWTS-G-DVLCCTASILHLVAIALDRYWAVTNI-DYIHASTAK-R
-                                                                            
+14==            A--LGHLGCQIFGIIGSYTGIAAGA-TNAFIAYDRFNVITRPMEG-K-MTHGKAIAMIIF
+15==            A--LGHLGCQIFGVIGSYTGIAAGA-TNAFIAYDRYNVITRPMEG-K-MTHGKAIAMIIF
+16==            AIYLGNTWCQIFASIGSYSGIGAGM-TNAAIGYDRYNVITKPMNR-N-MTFTKAVIMNII
+17==            A--LGNTWCQIFASIGSYSGIGAGM-TNAAIGYDRYNVITKPMNR-N-MTFTKAVIMNII
+18==            VWMFSPQYCEIYACLGAITGVC-SIWLLCMISFDRYNIICNGFNG-PKLTTGKAVVFALI
+19==            RWMFSGTYCEIYAALGAITGVC-SIWTLCMISFDRYNIICNGFNG-PKLTQGKATFMCGL
+20==            TWVLGPMMCDIYAGLGSAFG-CSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLALGKM--
+21==            TWVLGPMMCDIYAGLGSAFG-CSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLALGKIAY
+22==            TWVLGPMMCDIYAGLGSAFG-CSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLALGKIAY
+23==            TWVLGPLWCDIYAGCGSLFG-CVSIWSMCMIAFDRYNVIVKGING-TPMTIKTSIMKILF
+24==            TWVLGPLWCDIYAACGSLFG-CVSIWSMCMIAFDRYNVIVKGING-TPMTIKTSIMKIAF
+25==            TWVLGPLFCQIYAMLGSLFG-CGSIWTMTMIAFDRYNVIVKGLSG-KPLSINGALIRIIA
+26==            TWILGPFMCEVYGMAGSLFG-CASIWSMVMITLDRYNVIVRGMAA-APLTHKKATLLLLF
+27==            KWIFGKVACQLYGLLGGIFG-FMSINTMAMISIDRYNVIGRPMAASKKMSHRRAFLMIIF
+28==            KWIFGFAACKVYGFIGGIFG-FMSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFIMIIF
+1==             -FVFGPTMCSIEGFFATLGG-EVALWSLVVLAIERYIVICKPM-GNFRFGNTHAIMGVAF
+2==             -FVFGPTGCNLEGFFATLGG-EIGLWSLVVLAIERYVVVCKPM-SNFRFGENHAIMGVAF
+4=p             -FVLGPTGCAVEGFMATLGG-EVALWSLVVLAIERYIVVCKPM-GSFKFSSSHAFAGIAF
+5=p             -FALGPTGCAVEGFMATLGG-EVALWSLVVLAIERYIVVCKPM-GSFKFSSTHASAGIAF
+3==             -FVFGPVGCAVEGFFATLGG-QVALWSLVVLAIERYIVVCKPM-GNFRFSATHAMMGIAF
+6==             -FIFGATACKIEGFLATLGG-MVGLWSLAVVAFERWLVICKPL-GNFTFKTPHAIAGCIL
+7==             -FVFGRHVCALEGFLGTVAG-LVTGWSLAFLAFERYIVICKPF-GNFRFSSKHALTVVLA
+9==             -FVLGHPMCVLEGYTVSLCG-ITGLWSLAIISWERWMVVCKPF-GNVRFDAKLAIVGIAF
+10==            -FVLGHPMCVLEGYTVSLCG-ITGLWSLAIISWERWLVVCKPF-GNVRFDAKLAIVGIAF
+8=opsin_        -FVLGHPMCVLEGYTVSLCG-ITGLWSLAIISWERWLVVCKPF-GNVRFDAKLAIVGIAF
+11==            -FILGHPLCVIEGYVVSSCG-ITGLWSLAIISWERWFVVCKPF-GNIKFDSKLAIIGIVF
+12==            -FILGHPMCVVEGYTVSACG-ITALWSLAIISWERWFVVCKPF-GNIKFDGKLAVAGILF
+13==            -FVFGRRMCELEGFMVSLTG-IVGLWSLAILALERYVVVCKPL-GDFQFQRRHAVSGCAF
+30==            KWIFGHFFCNVFIAMDVMCC-TASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILS
+31=p            KWIFGHFFCNVFIAMDVMCC-TASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILS
+29==            KWIFGHFFCNVFIAMDVMCC-TASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILS
+32==            KWTLGQVTCDLFIALDVLCC-TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISL
+33=p            KWTLGQVTCDLFIALDVLCC-TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISL
+34==            VWFLHSEVCDMWISVDVLCC-TASILHLVAIAMDRYWAVTS-IDYIRRRSARRILLMIMV
+35=p            VWFLHSEVCDMWISVDVLCC-TASILHLVAIAMDRYWAVTS-IDYIRRRSARRILLMIMV
+36==            RWTLGPELCDMWTSGDVLCC-TASILHLVAIALDRYWAVTN-IDYIHASTAKRVGMMIAC
+                   :    * :                   :  :*:  :   :                 
 
-14==            EGK-MT--HGKAI-AMII-FIYMYA--TPWVVACYTET------WGRF---VPEGYLT--
-15==            EGK-MT--HGKAI-AMII-FIYLYA--TPWVVACYTES------WGRF---VPEGYLT--
-16==            NRN-MTFTKAVI--MNII-IWLYC---TPWVVLPLTQF------WDRF---VPEGYLT--
-17==            NRN-MTFTKAVI--MNII-IWLYC---TPWVVLPLTQF------WDRF---VPEGYLT--
-18==            GPK---LTTGKA--VVF---ALISW-VIAIGCALPPFF-----GW-GN---YILEGIL--
-19==            GPK---LTQGKATFMC-------GL-AWVISVGWSLPPF---FGW-GS---YTLEGIL--
-20==            AG-------RPMTIPL----ALGK----------------------MY---VPEGNLT--
-21==            AG-------RPMTIPL----ALGKI-AYIWFMSSIWCL-APAFGWSRY---VPEGNLT--
-22==            AG-------RPMTIPL----ALGKI-AYIWFMSTIWCCLAPVFGWSRY---VPEGNLT--
-23==            NGTPMTIKTSIMKILFIW--MMAVF-WTVMPLI----------GWSAY---VPEGNLT--
-24==            NGTPMTIKTSIMKIAFIW--MMAVF-WTIMPLI----------GWSSY---VPEGNLT--
-25==            GKPLS---INGALIRIIA-IWLFSLGWTIAPMF----------GWNRY---VPEGNMT--
-26==            AA--APLTHKKATLLLLF-VWIWSGGWTILPFF----------GWSRY---VPEGNLT--
-27==            SKKMS---HRRAFLMIIF-VWMWSI---VWSVGPVF-------NWGAY---VPEGILT--
-28==            SKKMS---HRRAFIMIIF-VWLWS-----VLWAIGPIF-----GWGAY---TLEGVLC--
-9==             GNVRF--DAKLAI-VGIAFSWIWAAVWTAPPI----------FGWSRY---WPHGLKT--
-10==            GNVRF--DAKLAI-VGIAFSWIWSAVWTAPPI----------FGWSRY---WPHGLKT--
-8=opsin_        GNVRF--DAKLAI-VGIAFSWIWAAVWTAPPI----------FGWSRY---WPHGLKT--
-11==            GNIKF--DSKLAI-IGIVFSW---VWAWGWSAPPI-------FGWSRY---WPHGLKT--
-12==            GNIKF--DGKLAV-AGILFSWLWSCAWTAPPI----------FGWSRY---WPHGLKT--
-1==             GNFRF--GNTHAI-MG---VAFTWIMA-LACAAPPL------VGWSRY---IPEGMQC--
-2==             SNFRF--GENHAI-MG---VAFTWVMA-LACAAPPL------VGWSRY---IPEGMQC--
-4=p             GSFKF--SSSHAF-AG---IAFTWVMA-LACAAPPL------FGWSRY---IPEGMQC--
-5=p             GSFKF--SSTHAS-AG---IAFTWVMA-MACAAPPL------VGWSRY---IPEGIQC--
-3==             GNFRF--SATHAM-MG---IAFTWVMAFS-CAAPPL------FGWSRY---MPEGMQC--
-6==             GNFTF--KTPHAI-AG---CILPWISALAASLPPLF-------GWSRY---IPEGLQC--
-7==             GNFRF--SSKHALTVV---LATWTI-GIGVSIPPFF-------GWSRF---IPEGLQC--
-13==            GDFQFQ-RRHAVS--G---CAFTWGWALLWSAPPLL-------GWSSY---VPEGLRT--
-30==            AK---MILSVWLLS-A---SITLPPLFGWAQNVNDDKVCLI-SQDFGYTIYSTAVAFYIP
-31=p            AK---MILSVWLLS-A---SITLPPLFGWAQNVNDDKVCLI-SQDFGYTIYSTAVAFYIP
-29==            AK---MILSVWLLS-A---SITLPPLFGWAQNVNDDKVCLI-SQDFGYTIYSTAVAFYIP
-32==            AA---ALISLTWLI-GFLISIPPMLGWRTPEDRSDPDACTI-SKDHGYTIYSTFGAFYIP
-33=p            AA---ALISLTWLI-GFLISIPPMLGWRTPEDRSDPDACTI-SKDHGYTIYSTFGAFYIP
-34==            RRILLMIMVVWIV--ALFISIPPLFGWRDPNNDPDKTGTCIISQDKGYTIFSTVGAFYLP
-35=p            RRILLMIMVVWIV--ALFISIPPLFGWRDPNNDPDKTGTCIISQDKGYTIFSTVGAFYLP
-36==            VGMMIA-CVWTVSFFV---CIAQLLGWKDPDWNQRV------SEDLRC-VVSQDVGYQIF
-                                                                            
+14==            IYMYATPWV-VACYTETW------GRFVPEGYLTSCTFDYLT--DNFDTRLFVACIFFFS
+15==            IYLYATPWV-VACYTESW------GRFVPEGYLTSCTFDYLT--DNFDTRLFVACIFFFS
+16==            IWLYCTPWV-VLPLTQFW------DRFVPEGYLTSCSFDYLS--DNFDTRLFVGTIFFFS
+17==            IWLYCTPWV-VLPLTQFW------DRFVPEGYLTSCSFDYLS--DNFDTRLFVGTIFLFS
+18==            SWVIAIGCA-LPPFF-GW------GNYILEGILDSCSYDYLT--QDFNTFSYNIFIFVFD
+19==            AWVISVGWS-LPPFF-GW------GSYTLEGILDSCSYDYFT--RDMNTITYNICIFIFD
+20==            --------------------------YVPEGNLTSCGIDYLE--RDWNPRSYLIFYSIFV
+21==            IWFMSSIWC-LAPAF-GW------SRYVPEGNLTSCGIDYLE--RDWNPRSYLIFYSIFV
+22==            IWFMSTIWCCLAPVF-GW------SRYVPEGNLTSCGIDYLE--RDWNPRSYLIFYSIFV
+23==            IWMMAVFWT-VMPLI-GW------SAYVPEGNLTACSIDYMT--RMWNPRSYLITYSLFV
+24==            IWMMAVFWT-IMPLI-GW------SSYVPEGNLTACSIDYMT--RQWNPRSYLITYSLFV
+25==            IWLFSLGWT-IAPMF-GW------NRYVPEGNMTACGTDYFN--RGLLSASYLVCYGIWV
+26==            VWIWSGGWT-ILPFF-GW------SRYVPEGNLTSCTVDYLT--KDWSSASYVVIYGLAV
+27==            VWMWSIVWS-VGPVF-NW------GAYVPEGILTSCSFDYLS--TDPSTRSFILCMYFCG
+28==            VWLWSVLWA-IGPIF-GW------GAYTLEGVLCNCSFDYIS--RDSTTRSNILCMFILG
+1==             TWIMALACA-APPLV-GW------SRYIPEGMQCSCGPDYYTLNPNFNNESYVVYMFVVH
+2==             TWVMALACA-APPLV-GW------SRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVH
+4=p             TWVMALACA-APPLF-GW------SRYIPEGMQCSCGPDYYTLNPDYNNESYVIYMFVCH
+5=p             TWVMAMACA-APPLV-GW------SRYIPEGIQCSCGPDYYTLNPEYNNESYVLYMFICH
+3==             TWVMAFSCA-APPLF-GW------SRYMPEGMQCSCGPDYYTHNPDYHNESYVLYMFVIH
+6==             PWISALAAS-LPPLF-GW------SRYIPEGLQCSCGPDWYTTNNKYNNESYVMFLFCFC
+7==             TWTIGIGVS-IPPFF-GW------SRFIPEGLQCSCGPDWYTVGTKYRSESYTWFLFIFC
+9==             SWIWAAVWT-APPIF-GW------SRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTC
+10==            SWIWSAVWT-APPIF-GW------SRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTC
+8=opsin_        SWIWAAVWT-APPIF-GW------SRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTC
+11==            SWVWAWGWS-APPIF-GW------SRYWPHGLKTSCGPDVFSGSVELGCQSFMLTLMITC
+12==            SWLWSCAWT-APPIF-GW------SRYWPHGLKTSCGPDVFSGSSDPGVQSYMVVLMVTC
+13==            TWGWALLWS-APPLL-GW------SSYVPEGLRTSCGPNWYTGGS--NNNSYILSLFVTC
+30==            VWLLSASIT-LPPLF-GW-----AQNVNDDKV---CLIS--------QDFGYTIYSTAVA
+31=p            VWLLSASIT-LPPLF-GW-----AQNVNDDKV---CLIS--------QDFGYTIYSTAVA
+29==            VWLLSASIT-LPPLF-GW-----AQNVNDDKV---CLIS--------QDFGYTIYSTAVA
+32==            TWLIGFLIS-IPPML-GWRTPE--DRSDPDA----CTIS--------KDHGYTIYSTFGA
+33=p            TWLIGFLIS-IPPML-GWRTPE--DRSDPDA----CTIS--------KDHGYTIYSTFGA
+34==            VWIVALFIS-IPPLF-GWRDPN-N---DPDKTG-TCIIS--------QDKGYTIFSTVGA
+35=p            VWIVALFIS-IPPLF-GWRDPN-N---DPDKTG-TCIIS--------QDKGYTIFSTVGA
+36==            VWTVSFFVC-IAQLL-GWKDPDWNQRVSEDL---RCVVS--------QDVGYQIFATASS
+                                             .     *  .                     
 
-14==            --SC--TF-DYLT-------DN-FDTRLF-----VACIFFF--SF---------VC----
-15==            --SC--TF-DYLT-------DN-FDTRLF-----VACIFFF--SF---------VC----
-16==            --SCSFDY-LS---------DN-FDTRLF-----VGTIFFF--SF---------VC----
-17==            --SCSFDY-LS---------DN-FDTRLF-----VGTIFLF--SF---------VV----
-18==            --DSC-SY-DYLT-------QD-FNTF-S-----Y-NIFIF--VF---------DY--FL
-19==            --DSC-SY-DYFT-------RD-MNTITY-----NICIFIF--DFFLP------AS----
-20==            --SC--GI-DYLE-------RD-WNPR-S-----YLIFY----SIF--------VY-YIP
-21==            --SC--GI-DYLE-------RD-WNPR-S-----YLIFY----SIF--------VY-YIP
-22==            --SC--GI-DYLE-------RD-WNPR-S-----YLIFY----SIF--------VY-YIP
-23==            --AC--SI-DYMT-------RM-WNPR-S-----YLITY----SLF--------VY-YTP
-24==            --AC--SI-DYMT-------RQ-WNPR-S-----YLITY----SLF--------VY-YTP
-25==            --AC--GT-DYFN-------RG-LLSA-S-----YLVCY----GIW--------VYFVPL
-26==            --SCT-V--DYLT-------KD-WSSA-S-----YVVIY----GLA--------VY---F
-27==            --SCSFDYLSTDP-------ST-RSFILC-----M-YFC----GFMLPIIIIAFCY----
-28==            --NCSFDYIS-RD-------STTRSNILC-----M-FIL----GFFGPILIIFFCY----
-9==             --SCGPDVFS--G-------SSYPGVQSY-----MIVLMVT--CCITPLSIIVLCYLQ--
-10==            --SCGPDVFS--G-------SSYPGVQSY-----MIVLMVT--CCIIPLAIIMLCYLQ--
-8=opsin_        --SCGPDVFS--G-------SSYPGVQSY-----MIVLMVT--CCITPLSIIVLCYLQ--
-11==            --SCGPDVFS--G-------SVELGCQSF-----MLTLMIT--CCFLPLFIIIVCYLQ--
-12==            --SCGPDVFS--G-------SSDPGVQSY-----MVVLMVT--CCFFPLAIIILCYLQ--
-1==             --SCGPDY-YTLN-------PNF-NNESY-----VVYMFVV--HFLVPFVIIFFCY----
-2==             --SCGIDY-YTLK-------PEV-NNESF-----VIYMFVV--HFTIPMIVIFFCY----
-4=p             --SCGPDY-YTLN-------PDY-NNESY-----VIYMFVC--HFILPVAVIFFTY----
-5=p             --SCGPDY-YTLN-------PEY-NNESY-----VLYMFIC--HFILPVTIIFFTY----
-3==             --SCGPDY-YTHN-------PDY-HNESY-----VLYMFVI--HFIIPVVVIFFSY----
-6==             --SCGPDW-YTTN-------NKY-NNESY-----VMFLFCF--CFAVPFGTIVFCY----
-7==             --SCGPDW-YTVG-------TKY-RSESYT----WFLFIFC--FIVPLSLICFSYTQLL-
-13==            --SCGPNW-YT-G-------GSN-NNSYIL----SLFVTCF--VLPL-SLILFSYT----
-30==            MSVMLFMYYQIYK----AARKSAAKHKFP--GFPRVQPE---SVISLN------GV-VKL
-31=p            MSVMLFMYYQIYK----AARKSAAKHKFP--GFPRVQPE---SVISLN------GV-VKL
-29==            MSVMLFMYYQIYK----AARKSAAKHKFP--GFPRVEP----DS-VIAL-----NGIVKL
-32==            LLLMLVLYGRIFR----AARFRIRKTVKKVEKTGADT------RHGASPAPQPKKSVNGE
-33=p            LLLMLVLYGRIFR----AARFRIRKTVRKVEKKGAGT------SLGTSSAPPPKKSLNGQ
-34==            MLVMMIIYIRIWL---VAR-SRIRKDKFQMTK-ARLKTEETTLVASPK---TEYSVVSDC
-35=p            MLVMMIIYIRIWL---VAR-SRIRKDKFQMTK-ARLKTEETTLVASPK---TEYSVVSDC
-36==            ATASSFYVPVLIILILYWRIYQTARKRIRR-R-RGAT-----ARGGVG---PPPVPAGG-
-                                                                            
+14==            FVCPTTMITYYYSQIVGHVFSHEKAL----------------------------------
+15==            FVCPTTMITYYYSQIVGHVFSHEKAL----------------------------------
+16==            FVCPTLMILYYYSQIVGHVFSHEKAL----------------------------------
+17==            FVVPTLMILYYYSQIVGHVFNHEKAL----------------------------------
+18==            YFLPAAIIVFSYVFIVKAIFAHEAAM----------------------------------
+19==            FFLPASVIVFSYVFIVKAIFAHEAAM----------------------------------
+20==            YYIPLFLICYSYWFIIAAVSAHEKAM----------------------------------
+21==            YYIPLFLICYSYWFIIAAVSAHEKAM----------------------------------
+22==            YYIPLFLICYSYWFIIAAVSAHEKAM----------------------------------
+23==            YYTPLFLICYSYWFIIAAVAAHEKAM----------------------------------
+24==            YYTPLFMICYSYWFIIATVAAHEKAM----------------------------------
+25==            YFVPLFLIIYSYWFIIQAVAAHEKNM----------------------------------
+26==            YFLPLITMIYCYFFIVHAVAEHEKQL----------------------------------
+27==            FMLPIIIIAFCYFNIVMSVSNHEKEM----------------------------------
+28==            FFGPILIIFFCYFNIVMSVSNHEKEM----------------------------------
+1==             FLVPFVIIFFCYGRLLCTV-----------------------------------------
+2==             FTIPMIVIFFCYGQLVFTV-----------------------------------------
+4=p             FILPVAVIFFTYGRLVCTV-----------------------------------------
+5=p             FILPVTIIFFTYGRLVCTV-----------------------------------------
+3==             FIIPVVVIFFSYGRLICKV-----------------------------------------
+6==             FAVPFGTIVFCYGQLLITL-----------------------------------------
+7==             FIVPLSLICFSYTQLLRAL-----------------------------------------
+9==             CITPLSIIVLCYLQVWLAI-----------------------------------------
+10==            CIIPLAIIMLCYLQVWLAI-----------------------------------------
+8=opsin_        CITPLSIIVLCYLQVWLAI-----------------------------------------
+11==            CFLPLFIIIVCYLQVWMAI-----------------------------------------
+12==            CFFPLAIIILCYLQVWLAI-----------------------------------------
+13==            FVLPLSLILFSYTNLLLTL-----------------------------------------
+30==            FYIPMSVMLFMYYQIYKAARKSAAK--HKF-------------------P----------
+31=p            FYIPMSVMLFMYYQIYKAARKSAAK--HKF-------------------P----------
+29==            FYIPMSVMLFMYYQIYKAARKSAAK--HKF-------------------P----------
+32==            FYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADTRHGASP----APQPKKS----VN
+33=p            FYIPLLLMLVLYGRIFRAARFRIRKTVRKVEKKGAGTSLGTSS----APPPKKS----LN
+34==            FYLPMLVMMIIYIRIWLVARSRIRK--DKFQ--MTKARLKTEETTLVASPKTEY--SVVS
+35=p            FYLPMLVMMIIYIRIWLVARSRIRK--DKFQ--MTKARLKTEETTLVASPKTEY--SVVS
+36==            FYVPVLIILILYWRIYQTARKRIRR--RR----GATARGG------VGPPPVPAGGALVA
+                   *   :   *  :                                             
 
-14==            -----PTTMITYY-YSQIVGH--VFS-HEK--------AL---RDQAKKMN-VESLRS--
-15==            -----PTTMITYY-YSQIVGH--VFS-HEK--------AL---RDQAKKMN-VDSLRS--
-16==            -----PTLMILYY-YSQIVGH--VFS-HEK--------AL---REQAKKMN-VESLRS--
-17==            -----PTLMILYY-YSQIVGH--VFN-HEK--------AL---REQAKKMN-VESLRS--
-18==            PA---AIIVF-SY-VFI-VKAIFA-HEA----------AM---RAQAKKMN-VSTLRS--
-19==            -V---I--VF-SY-VFI-VKAIFA-HEA----------AM---RAQAKKMN-VTNLRS--
-20==            LF---LICY--SY-WFIIA-A--VSA-HEK--------AM---REQAKKMN-VKSLRS--
-21==            LF---LICY--SY-WFIIA-A--VSA-HEK--------AM---REQAKKMN-VKSLRS--
-22==            LF---LICY--SY-WFIIA-A--VSA-HEK--------AM---REQAKKMN-VKSLRS--
-23==            LF---LICY--SY-WFIIAAV--A-A-HEK--------AM---REQAKKMN-VKSLRS--
-24==            LF---MICY--SY-WFIIATV--A-A-HEK--------AM---RDQAKKMN-VKSLRS--
-25==            FL---IIYS--YW-FIIQA-V--A-A-HEK--------NM---REQAKKMN-VASLRS--
-26==            LP---LITMI-YC-YFFIV-H--AVAEHEK--------QL---REQAKKMN-V---ASL-
-27==            -F---NIVMSVSN-HEKEMAAM-AKRLNAKELRKAQ-AGA---SAEMKLAKIS---MVII
-28==            -F---NIVMSVSN-HEKEMAAM-AKRLNAKELRKAQ-AGA---NAEMRLAKISIVIVSQF
-9==             -------VWLAI---RAVA-KQ-QKESESTQ------KAE---KE-VTRMVVVMVLA---
-10==            -------VWLAI---RAVA-KQ-QKESESTQ------KAE---KE-VTRMVVVMIFA---
-8=opsin_        -------VWLAI---RAVA-KQ-QKESESTQ------KAE---KE-VTRMVVVMVLA---
-11==            -------VWMAI---RAVA-AQ-QKESESTQ------KAE---RE-V-SRMVVVMIV---
-12==            -------VWLAI---RAVA-AQ-QKESESTQ------KAE---KE-V-SRMVVVMIV---
-1==             -------GRLLCT-VKEAA-AA-QQESASTQ------KAE---KE-VTRMVVLMVIGFLV
-2==             -------GQLVFT-VKEAA-AQ-QQESATTQ------KAE---KE-VTRMVIIMVIFFLI
-4=p             -------GRLVCT-VKAAA-AQ-QQDSASTQ------KAE---RE-VTKMVILMVFGF-L
-5=p             -------GRLVCT-VKAAA-AQ-QQDSASTQ------KAE---RE-VTKMVILMVLGF-L
-3==             -------GRLICK-VREAA-AQ-QQESATTQ------KAE---KE-VTRMVILMVLGF-M
-6==             -------GQLLIT-LKLAAKAQ-A-DSASTQ------KAE---RE-VTKMVVVMVLGFLV
-7==             -------RAL-----KAVA-AQ-QQESATTQ------KAE---RE-VSRMVVVMVGSFCV
-13==            --------NLLLT-LRAAA-AQ-Q-KEADTTQ-----RAE---RE-VTRMVIVMV-----
-30==            QKEVEECANLSRL-LKHERKNI----SIFKREQ----KAATTLGII-VGAFTVCWLPF--
-31=p            QKEVEECANLSRL-LKHERKNI----SIFKREQ----KAATTLGII-VGAFTVCWLPF--
-29==            QKEVEECANLSRL-LKHERKNI----SIFKREQ----KAATTLGII-VGAFTVCWLPF--
-32==            SG-SR-NWRLGV--ESKAGGA---L-CANGAVRQGDDGAALE-VIEVHRVG-NSKEHL--
-33=p            PG-SG-DWR-RC--AENRAVG---TPC-TNGAVRQGDDEATLEVIEVHRVG-NSKEHL--
-34==            NG-C---NSPDSTTEKKKRRAP-FKSYGCSPRPERKKNRAKKLPE--NANG-VNSNSS--
-35=p            NG-C---NSPDSTTEKKKRRAP-FKSYGCSPRPERKKNRAKKLPE--NANG-VNSNSS--
-36==            AL-V---AGGGS---GGIAAA----VVAVIGRPLPTISETTTTGF--TNVS-SNNTSP--
+14==            ----------------------------RDQAKKM----------------NVES-----
+15==            ----------------------------RDQAKKM----------------NVDS-----
+16==            ----------------------------REQAKKM----------------NVES-----
+17==            ----------------------------REQAKKM----------------NVES-----
+18==            ----------------------------RAQAKKM----------------NVST-----
+19==            ----------------------------RAQAKKM----------------NVTN-----
+20==            ----------------------------REQAKKM----------------NVKS-----
+21==            ----------------------------REQAKKM----------------NVKS-----
+22==            ----------------------------REQAKKM----------------NVKS-----
+23==            ----------------------------REQAKKM----------------NVKS-----
+24==            ----------------------------RDQAKKM----------------NVKS-----
+25==            ----------------------------REQAKKM----------------NVAS-----
+26==            ----------------------------REQAKKM----------------NVAS-----
+27==            ----------------------------AAMAKRL----------------NAKE-----
+28==            ----------------------------AAMAKRL----------------NAKE-----
+1==             ----------------------------KEAAAA--------------------------
+2==             ----------------------------KEAAAQ--------------------------
+4=p             ----------------------------KAAAAQ--------------------------
+5=p             ----------------------------KAAAAQ--------------------------
+3==             ----------------------------REAAAQ--------------------------
+6==             ----------------------------KLAAKA--------------------------
+7==             ----------------------------KAVAAQ--------------------------
+9==             ----------------------------RAVAKQ--------------------------
+10==            ----------------------------RAVAKQ--------------------------
+8=opsin_        ----------------------------RAVAKQ--------------------------
+11==            ----------------------------RAVAAQ--------------------------
+12==            ----------------------------RAVAAQ--------------------------
+13==            ----------------------------RAAAAQ--------------------------
+30==            ------------------------G-FPRVQ---------PESVISLNGVVKLQK-----
+31=p            ------------------------G-FPRVQ---------PESVISLNGVVKLQK-----
+29==            ------------------------G-FPRVE---------PDSVIALNGIVKLQK-----
+32==            GESGSRNWRLGVESKAGGALCAN-G-AVRQGDDGAALEVIE-----VHRVGNSKEHLPL-
+33=p            GQPGSGDWRRCAENRAVGTPCTN-G-AVRQGDDEATLEVIE-----VHRVGNSKEHLPL-
+34==            DCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSSSERLKQI
+35=p            DCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSSSERLKQI
+36==            ---GGGSGGIAA------AVVAVIG---RP---------LP----------TISE-----
                                                                             
 
-14==            -----NVDKNKET----AEIRIAKAAI-TI----CFLFFC-----SWTP-YGV---MSLI
-15==            -----NVDKSKEA----AEIRIAKAAI-TI----CFLFFA-----SWTP-YGV---MSLI
-16==            -----NVDKSKET----AEIRIAKAAI-TI----CFLFFV-----SWTP-YGV---MSLI
-17==            -----NVDKSKET----AEIRIAKAAI-TI----CFLFFV-----SWTP-YGV---MSLI
-18==            -----NEA--DAQR---AEIRIAKTALVNV----SLWFI------CWTP-YALI---SLK
-19==            -----NEAE-TQ-R---AEIRIAKTALVNV----SLWFI------CWTP-YAAITIQGLL
-20==            ---SED-AE-K--S---AEGKLAKVALVTI----TLWF-------MAWTPYLVINCMGLF
-21==            ---SED-AE-K--S---AEGKLAKVALVTI----TLWF-------MAWTPYLVINCMGLF
-22==            ---SED-AD-K--S---AEGKLAKVALVTI----SLWF-------MAWTPYLVINCMGLF
-23==            ---SEDCD--K--S---AEGKLAKVALTTI----SLWF-------MAWTPYLVICYFGLF
-24==            ---SEDCD--K--S---AENKLAKVALTTI----SLWF-------MAWTPYLIICYFGLF
-25==            ---SENQN--T--S---AECKLAKVALMTI----SLWF-------MAWTPYLVINFSGIF
-26==            ---RANADQQKQ-S---AECRLAKVAMMTV----GLWF-------MAWTPYLIISWAGVF
-27==            TQFMLS-WSPYAIIALLAQFGPAEWVTPYAAELPVLFAKA-----SAIH-NPIVYSVSHP
-28==            L---LS-WSPYAVVALLAQFGPLEWVTPYAAQLPVMFAKA-----SAIH-NPMIYSVSHP
-9==             --FCFC-WGPYAFF---ACFAAANPGYPFHPLMAALPAFF---AKSAT-------IYNPV
-10==            --YCVC-WGPYTFF---ACFAAANPGYAFHPLMAALPAYF---AKSAT-------IYNPV
-8=opsin_        --FC--------------------------------------------------------
-11==            -AFCIC-WGPYASF---VSFAAANPGYAFHPLAAALPAYF---AKSAT-------IYNPV
-12==            -AYCFC-WGPYTFF---ACFAAANPGYAFHPLAAALPAYF---AKSAT-------IYNPI
-1==             CWVP-Y-A--SV-----AFYIFTHQGS----DFGATFMTL--PAFFA--K--SSALYNPV
-2==             CWLP-Y-A--SV-----AMYIFTHQGS----NFGPIFMTL--PAFFA--KTAS--IYNPI
-4=p             IAWTPY-AT-VA-----AWIFFNKGA-----DFS---AKF--MAIPAFFSK-SSALYNPV
-5=p             VAWTPY-AT-VA-----AWIFFNKGA-----AFS---AQF--MAIPAFFSK-TSALYNPV
-3==             LAWTPY-A--VV-----AFWIFTNKG-----A-DFT-ATL--MAVPAFFSK-SSSLYNPI
-6==             CWAP-Y-ASFSL-----WIVS-HRGEEF---DLRM--ATIPSCLSKA--ST-V---YNPV
-7==             CYVP-Y-A-AFA-----MYMV-NNRNH----GLDLRLVTIP-SFFS---KSAC--IYNPI
-13==            MAFLLC-WLPYSTF---ALVVATHKGIIIQPVLASLPSYF--S-KTAT-VY-NPIIYVFM
-30==            --FLLST------------ARPFICGT-------SC--SCIPLWVERTCLW-----LGYA
-31=p            --FLLST------------ARPFICGT-------SC--SCIPLWVERTCLW-----LGYA
-29==            --FLLST------------ARPFICGT-------SC--SCIPLWVERTFLW-----LGYA
-32==            --PLPSE------------AGP--TPCAPA----SFERKNER-NAEAK-RK-----MALA
-33=p            --PLPSES-----------GS---NSYAPA----CLERKNER-NAEAK-RK-----MALA
-34==            --SSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKIS-SN-DT-PY-----SRTR
-35=p            --SSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKIS-SN-DT-PY-----SRTR
-36==            --EKQS-------CANGLEADPPTTGY-GA----VAAAYYPSLVR-RK-PK-----EA-A
+14==            ---------------------LRSNV-DKNKE----------------------------
+15==            ---------------------LRSNV-DKSKE----------------------------
+16==            ---------------------LRSNV-DKSKE----------------------------
+17==            ---------------------LRSNV-DKSKE----------------------------
+18==            ---------------------LRSNEADAQR-----------------------------
+19==            ---------------------LRSNEAETQR-----------------------------
+20==            ---------------------LRSSE-DAEK-----------------------------
+21==            ---------------------LRSSE-DAEK-----------------------------
+22==            ---------------------LRSSE-DADK-----------------------------
+23==            ---------------------LRSSE-DCDK-----------------------------
+24==            ---------------------LRSSE-DCDK-----------------------------
+25==            ---------------------LRSSE-NQNT-----------------------------
+26==            ---------------------LRANA-DQQKQ----------------------------
+27==            ---------------------LRKAQ---AGA----------------------------
+28==            ---------------------LRKAQ---AGA----------------------------
+1==             ----------------------QQESASTQK-----------------------------
+2==             ----------------------QQESATTQK-----------------------------
+4=p             ----------------------QQDSASTQK-----------------------------
+5=p             ----------------------QQDSASTQK-----------------------------
+3==             ----------------------QQESATTQK-----------------------------
+6==             ----------------------QADSASTQK-----------------------------
+7==             ----------------------QQESATTQK-----------------------------
+9==             ----------------------QKESESTQK-----------------------------
+10==            ----------------------QKESESTQK-----------------------------
+8=opsin_        ----------------------QKESESTQK-----------------------------
+11==            ----------------------QKESESTQK-----------------------------
+12==            ----------------------QKESESTQK-----------------------------
+13==            ----------------------QKEADTTQR-----------------------------
+30==            ---------------------EVEECAN------------------------LSRLLKHE
+31=p            ---------------------EVEECAN------------------------LSRLLKHE
+29==            ---------------------EVEECAN------------------------LSRLLKHE
+32==            ---PSEAGPTPCA----PASFERKNERNAEA----------------------KR-----
+33=p            ---PSESGSNSYA----PACLERKNERNAEA----------------------KR-----
+34==            QIETAEAFANGCAEEASIAMLERQ-CNNGKKISSNDTP---Y---------SRTR----E
+35=p            QIETAEAFANGCAEEASIAMLERQ-CNNGKKISSNDTP---Y---------SRTR----E
+36==            --TTTTGFTNVSSNNTSP---EKQSCANGLE---ADPPTTGYGAVAAAYYPSLVRRKPKE
                                                                             
 
-14==            G-AF-G--DKTLL----TPGA-T----MIPACAC--KM-VACIDPF--VYAI-S-HPRYR
-15==            G-AF-G--DKTLL----TPGA-T----MIPACTC--KM-VACIDPF--VYAI-S-HPRYR
-16==            G-AF-G--DKSLL----TQGA-T----MIPACTC--KL-VACIDPF--VYAI-S-HPRYR
-17==            G-AF-G--DKSLL----TPGA-T----MIPACTC--KL-VACIEPF--VYAI-S-HPRYR
-18==            GVMG-D---TSGI----TPLVSTLP-AL-LA-K---S--CSCYNPF--VYAI-S-HPKYR
-19==            GNAE-G--ITPLL----T----TLP-AL-LA-K---S--CSCYNPF--VYAI-S-HPKFR
-20==            KFE--G--LTPLN----TI---W---GACFA-K---SA-ACYNPI---VYGI-S-HPKYR
-21==            KFE--G--LTPLN----TI---W---GACFA-K---SA-ACYNPI---VYGI-S-HPKYR
-22==            KFE--G--LTPLN----TI---W---GACFA-K---SA-ACYNPI---VYGI-S-HPKYR
-23==            KID--G--LTPLT----TI---W---GATFA-KT--SA-VYNPI----VYGI-S-HPKYR
-24==            KID--G--LTPLT----TI---W---GATFA-KT--SA-VYNPI----VYGI-S-HPNDR
-25==            NLV--K--ISPLF----TI---W---GSLFA-KA--NA-VYNPI----VYGI-S-HPKYR
-26==            SSGT-R--LTPLA----TI---W---G--SV-FA--KA-NSCYNPI--VYGI-S-HPRYK
-27==            KFRE-AIQTTFPWLLTCCQFDEKECEDANDAEEE---V-VASERGGESRDAAQM-KEMMA
-28==            KFRE-AISQTFPWVLTCCQFDDKETEDDKDAETEI-PA-GESSDAAPSADAAQM-KEMMA
-9==             IYVF----MNRQF--RNCIL--QL-----FGKK--------VDDGSELSSA--S-KTEVS
-10==            IYVF----MNRQF--RNCIL--QL-----FGKK--------VDDGSELSSA--S-KTEVS
+14==            -------TAEIRIAKAAITICFLFFCSWTPYGVM-SLIGAF----GDKTLLTPGATMIPA
+15==            -------AAEIRIAKAAITICFLFFASWTPYGVM-SLIGAF----GDKTLLTPGATMIPA
+16==            -------TAEIRIAKAAITICFLFFVSWTPYGVM-SLIGAF----GDKSLLTQGATMIPA
+17==            -------TAEIRIAKAAITICFLFFVSWTPYGVM-SLIGAF----GDKSLLTPGATMIPA
+18==            --------AEIRIAKTALVNVSLWFICWTPYALI-SLKGVMGDTSG----ITPLVSTLPA
+19==            --------AEIRIAKTALVNVSLWFICWTPYAAI-TIQGLLGNAEG----ITPLLTTLPA
+20==            -------SAEGKLAKVALVTITLWFMAWTPYLVINCM-GLF-KFEG----LTPLNTIWGA
+21==            -------SAEGKLAKVALVTITLWFMAWTPYLVINCM-GLF-KFEG----LTPLNTIWGA
+22==            -------SAEGKLAKVALVTISLWFMAWTPYLVINCM-GLF-KFEG----LTPLNTIWGA
+23==            -------SAEGKLAKVALTTISLWFMAWTPYLVI-CYFGLF-KIDG----LTPLTTIWGA
+24==            -------SAENKLAKVALTTISLWFMAWTPYLII-CYFGLF-KIDG----LTPLTTIWGA
+25==            -------SAECKLAKVALMTISLWFMAWTPYLVI-NFSGIF-NLVK----ISPLFTIWGS
+26==            -------SAECRLAKVAMMTVGLWFMAWTPYLII-SWAGVF-S-SGTR--LTPLATIWGS
+27==            -------SAEMKLAKISMVIITQFMLSWSPYAII-ALLAQF----GPAEWVTPYAAELPV
+28==            -------NAEMRLAKISIVIVSQFLLSWSPYAVV-ALLAQF----GPLEWVTPYAAQLPV
+1==             --------AEKEVTRMVVLMVIGFLVCWVPYASVAFYIFTH---QGSD--FGATFMTLPA
+2==             --------AEKEVTRMVIIMVIFFLICWLPYASVAMYIFTH---QGSN--FGPIFMTLPA
+4=p             --------AEREVTKMVILMVFGFLIAWTPYATVAAWIFFN---KGAD--FSAKFMAIPA
+5=p             --------AEREVTKMVILMVLGFLVAWTPYATVAAWIFFN---KGAA--FSAQFMAIPA
+3==             --------AEKEVTRMVILMVLGFMLAWTPYAVVAFWIFTN---KGAD--FTATLMAVPA
+6==             --------AEREVTKMVVVMVLGFLVCWAPYASFSLWIVSH---RGEE--FDLRMATIPS
+7==             --------AEREVSRMVVVMVGSFCVCYVPYAAFAMYMVNN---RNHG--LDLRLVTIPS
+9==             --------AEKEVTRMVVVMVLAFCFCWGPYAFFACFAAAN---PGYP--FHPLMAALPA
+10==            --------AEKEVTRMVVVMIFAYCVCWGPYTFFACFAAAN---PGYA--FHPLMAALPA
+8=opsin_        --------AEKEVTRMVVVMVLAFC-----------------------------------
+11==            --------AEREVSRMVVVMIVAFCICWGPYASFVSFAAAN---PGYA--FHPLAAALPA
+12==            --------AEKEVSRMVVVMIVAYCFCWGPYTFFACFAAAN---PGYA--FHPLAAALPA
+13==            --------AEREVTRMVIVMVMAFLLCWLPYSTFALVVATH---KGII--IQPVLASLPS
+30==            RKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFI--CGTSCSCIPLWVERTCL
+31=p            RKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFI--CGTSCSCIPLWVERTCL
+29==            RKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFI--CGTSCSCIPLWVERTFL
+32==            KMAL---ARERKTVKTLGIIMGTFILCWLPFFIVALVLPF---CESSCH-MPTLLGAIIN
+33=p            KMAL---ARERKTVKTLGIIMGTFILCWLPFFIVALVLPF---CESSCH-MPALLGAIIN
+34==            KLEL---KRERKAARTLAIITGAFLICWLPFFIIALIGPF---VD--PEGIPPFARSFVL
+35=p            KLEL---KRERKAARTLAIITGAFLICWLPFFIIALIGPF---VD--PEGIPPFARSFVL
+36==            AADS---KRERKAAKTLAIITGAFVACWLPFFVLAILVPT---CD--CE-VSPVLTSLSL
+                         * .           :                                    
+
+14==            CACKMVACIDPFVYAISHPRYRMELQKRCP--WLALNE--KAPESSAVASTSTTQEP-QQ
+15==            CTCKMVACIDPFVYAISHPRYRMELQKRCP--WLAISE--KAPESRAAISTSTTQEQ-QQ
+16==            CTCKLVACIDPFVYAISHPRYRLELQKRCP--WLGVNE--KSGEISSAQST-TTQEQ-QQ
+17==            CTCKLVACIEPFVYAISHPRYRMELQKRCP--WLGVNE--KSGEASSAQST-TTQEQTQQ
+18==            LLAKSCSCYNPFVYAISHPKYRLAITQHLP--WFCV-H--ETETKSND----DSQSN--S
+19==            LLAKSCSCYNPFVYAISHPKFRLAITQHLP--WFCV-H--EKDP--NDV--EENQSS--N
+20==            CFAKSAACYNPIVYGISHPKYRLALKEKCP---CCVFG--KVD----DGKSSDAQSQ--A
+21==            CFAKSAACYNPIVYGISHPKYRLALKEKCP---CCVFG--KVD----DGKSSDAQSQ--A
+22==            CFAKSAACYNPIVYGISHPKYRLALKEKCP---CCVFG--KVD----DGKSSEAQSQ--A
+23==            TFAKTSAVYNPIVYGISHPKYRIVLKEKCP---MCVFG--NTDEPKPDAPASDTE-----
+24==            TFAKTSAVYNPIVYGISHPNDRLVLKEKCP---MCVCG--TTDEPKPDAPPSDTE-----
+25==            LFAKANAVYNPIVYGISHPKYRAALFAKFPS-LACA------AEPSSDA-VSTTSGT--T
+26==            VFAKANSCYNPIVYGISHPRYKAALYQRFPS-LACGSG-----ESGSDV---KSEAS--A
+27==            LFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQF--DEKE-CEDANDAEEEVVASE
+28==            MFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQF--DDKE-TEDDKDAETEIPAGE
+1==             FFAKSSALYNPVIYILMNKQFRNCMITTLC----CGKNPLGDDE--SGASTSKTEVSSVS
+2==             FFAKTASIYNPIIYIMMNKQFRNCMLTSLC----CGKNPLGDDE--ASATASKTE-----
+4=p             FFSKSSALYNPVIYVLLNKQFRNCMLTTIF----CGKNPLGDDE-SSTVSTSKTEVSSVS
+5=p             FFSKTSALYNPVIYVLLNKQFRSCMLTTLF----CGKNPLGDEE-SSTVSTSKTEVSSVS
+3==             FFSKSSSLYNPIIYVLMNKQFRNCMITTIC----CGKNPFGDEDVSSTVSQSKTEVSSVS
+6==             CLSKASTVYNPVIYVLMNKQFRSCMMKMV-----CGKN-IEEDE--ASTSSQVTQVSSVA
+7==             FFSKSACIYNPIIYCFMNKQFQACIMKMV-----CGKA-MTDES--DTCSSQKTEVSTVS
+9==             FFAKSATIYNPVIYVFMNRQFRNCILQLF------G---KKVDDGSELSSASKTEVSSVS
+10==            YFAKSATIYNPVIYVFMNRQFRNCILQLF------G---KKVDDGSELSSASKTEVSSVS
 8=opsin_        ------------------------------------------------------------
-11==            IYVF----MNRQF--RNCIM--QL-----FGKK--------VDDGSEASTT--S-RTEVS
-12==            IYVF----MNRQF--RNCIL--QL-----FGKK--------VDDGSEVST---S-RTEVS
-1==             IYIL----MNKQF--RNCMI--TT---LCCGKNPL-GDDE-SG-A---ST---S-KTEVS
-2==             IYIM----MNKQF--RNCML--TS---LCCGKNPL-GDDEASATA---SK-----TETSQ
-4=p             IYVL----LNKQF--RNCML--TT---IFCGKNPL-GD-DESSTV---ST---S-KTEVS
-5=p             IYVL----LNKQF--RSCML--TT---LFCGKNPL-GD-EESSTV---ST---S-KTEVS
-3==             IYVL----MNKQF--RNCMI--TT---ICCGKNPF-GDEDVSSTV---SQ---S-KTEVS
-6==             IYVL----MNKQF--RSCMM--K----MVCGKNIE-EDEA--STS---SQ---V-TQVSS
-7==             IYCF----MNKQFQ-ACIM----K---MVCGKA----MTDESDTC---SS---Q-KTEVS
-13==            NKQF-Q--SCLLE--MLCCG--YQP--QRTGKASP-GTPGPHADVTAAGL---R-NK-VM
-30==            NSLI-NPFIY--AFFNRDLR-PT------SRS------LLQCQYRNINRKLSAA---GMH
-31=p            NSLI-NPFIY--AFFNRDLR-TT------YRS------LLQCQYRNINRKLSAA---GMH
-29==            NSLI-NPFIY--AFFNRDLR-TT------YRS------LLQCQYRNINRKLSAA---GMH
-32==            RE---RKTVKTLGIIMGTFILCWLP-FFIVAL-----VLPFCESSCHMPTLLGA-IIN-W
-33=p            RE---RKTVKTLGIIMGTFILCWLP-FFIVAL-----VLPFCESSCHMPALLGA-IIN-W
-34==            EKLELKRERK--A--ARTLAIITGA-FLICWLPFFIIALIGPFVDPEGIPPFAR-SFVLW
-35=p            EKLELKRERK--A--ARTLAIITGA-FLICWLPFFIIALIGPFVDPEGIPPFAR-SFVLW
-36==            DS---KRERK--A--AKTLAIITGA-FVACWLPFFVLAILVPTCDCEVSP--VLTSLSLW
+11==            YFAKSATIYNPVIYVFMNRQFRNCIMQLF------G---KKVDDGSEASTTSRTEVSSVS
+12==            YFAKSATIYNPIIYVFMNRQFRNCILQLF------G---KKVDDGSEVST-SRTEVSSVS
+13==            YFSKTATVYNPIIYVFMNKQFQSCLLEMLC----CGYQPQRTGKASPGTPGPHADVTAAG
+30==            WLGYANSLINPFIYAFFNRDLRPTSRSLLQ----CQY-RNINRKLSAAGMHEALKLAERP
+31=p            WLGYANSLINPFIYAFFNRDLRTTYRSLLQ----CQY-RNINRKLSAAGMHEALKLAERP
+29==            WLGYANSLINPFIYAFFNRDLRTTYRSLLQ----CQY-RNINRKLSAAGMHEALKLAERP
+32==            WLGYSNSLLNPVIYAYFNKDFQNAFKKIIK----CKFCRQ--------------------
+33=p            WLGYSNSLLNPVIYAYFNKDFQNAFKKIIK----CKFCRR--------------------
+34==            WLGYFNSLLNPIIYTIFSPEFRSAFQKIL-----FGKYRRGHR-----------------
+35=p            WLGYFNSLLNPIIYTIFSPEFRSAFQKIL-----FGKYRRGHR-----------------
+36==            WLGYFNSTLNPVIYTVFSPEFRHAFQRLL-----CG--RRVRRRRAPQ------------
                                                                             
 
-14==            MELQKR--CPW-LAL--NE------K----APES-SAVA--STSTTQEPQ---QTT-AA-
-15==            MELQKR--CPW-LAI--SE------K----APES-RAAI--STSTTQEQQ---QTT-AA-
-16==            LELQKR--CPW-LGV--NE------KS---GEIS-SAQ---ST-TTQEQQ---QTT-AA-
-17==            MELQKR--CPW-LGV--NE------KS---GEAS-SAQ---ST-TTQEQT---QQTSAA-
-18==            LAITQHL--PWFCVHETET------KS---NDDSQSNS-------TV-AQ---DK---A-
-19==            LAITQHL--PWFCVHEKDP------ND---VEENQSSN-------TQTQE---KS-----
-20==            LALKEKCPCCV-FG---KV------DD---GKSS-DAQ---SQATASEAE---SK---A-
-21==            LALKEKCPCCV-FG---KV------DD---GKSS-DAQ---SQATASEAE---SK---A-
-22==            LALKEKCPCCV-FG---KV------DD---GKSS-EAQ---SQATTSEAE---SK---A-
-23==            IVLKEKCPMCV-FG---N-------TD---EPKP-DAPA-SDTETTSEAD---SK---A-
-24==            LVLKEKCPMCV-CG---T-------TD---EPKP-DAPP-SDTETTSEAE---SK---D-
-25==            AALFAKFPSLA-CAAEPSS------DA---VSTT-SGT---TTVTDNE-K---SN---A-
-26==            AALYQRFPSLA-CGSGESG------SD---VKSEASAT------TTMEEK---PKIPEA-
-27==            MMQK----MQAQQAA--YQPPPPPQGYPPQGYPPQGAYP-PPQGYPPQGYPPQGYPPQGY
-28==            MMQK----MQQQQAA--YPPQ----GY---APPPQG-YP-PQ-GYPPQGYPPQGYPPQGY
-9==             SVSSVS----P--A----------------------------------------------
-10==            SVSSVS----P--A----------------------------------------------
+14==            TTAA--------------------------------------------------------
+15==            TTAA--------------------------------------------------------
+16==            TTAA--------------------------------------------------------
+17==            TSAA--------------------------------------------------------
+18==            TVAQDKA-----------------------------------------------------
+19==            TQTQEKS-----------------------------------------------------
+20==            TASEAE-SKA--------------------------------------------------
+21==            TASEAE-SKA--------------------------------------------------
+22==            TTSEAE-SKA--------------------------------------------------
+23==            TTSEAD-SKA--------------------------------------------------
+24==            TTSEAE-SKD--------------------------------------------------
+25==            TVTDNEKSNA--------------------------------------------------
+26==            TTTMEEKPKIPEA-----------------------------------------------
+27==            R--GGESRDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGY--PPQGYPPQGAYPPPQGYPP
+28==            SSDAAPSADAAQMKEMMAMMQKMQQQQAAY----PPQGYAPPPQGYPPQG-YPP-QGYPP
+1==             T-SPVSPA----------------------------------------------------
+2==             T-SQVAPA----------------------------------------------------
+4=p             ------PA----------------------------------------------------
+5=p             ------PA----------------------------------------------------
+3==             S-SQVSPA----------------------------------------------------
+6==             ------PEK---------------------------------------------------
+7==             S-TQVGPN----------------------------------------------------
+9==             ---SVSPA----------------------------------------------------
+10==            ---SVSPA----------------------------------------------------
 8=opsin_        ------------------------------------------------------------
-11==            SVSNSS----V--APA--------------------------------------------
-12==            SVSNSS----VSPA----------------------------------------------
-1==             SVSTSP----VSPA----------------------------------------------
-2==             VAP-------A-------------------------------------------------
-4=p             SVSP------A-------------------------------------------------
-5=p             SVSP------A-------------------------------------------------
-3==             SVSSSQ----VSPA----------------------------------------------
-6==             VAPEK-------------------------------------------------------
-7==             TVSSTQ----VGPN----------------------------------------------
-13==            PAHP------V-------------------------------------------------
-30==            EALKLAE---RPERSEFVLQ-N---SDH-----CGK----KGHD-T--------------
-31=p            EALKLAE---RPERSEFVLQ-N---SDH-----CGK----KGHD-T--------------
-29==            EALKLAE---RPERPEFVLQ-N---ADY-----CRK----KGHDS---------------
-32==            LG-YSN----SLLN--PVIYAY--FNKDFQNAF-KKIIKCKFCRQ---------------
-33=p            LG-YSN----SLLN--PVIYAY--FNKDFQNAF-KKIIKCKFCRR---------------
-34==            LG-YFN----SLLNPIIYTIFSPEFRSAFQKILFGK-YR-RGHR----------------
-35=p            LG-YFN----SLLNPIIYTIFSPEFRSAFQKILFGK-YR-RGHR----------------
-36==            LG-YFN----STLNPVIYTVFSPEFRHAFQRLLCGRRVR-RRRAPQ--------------
+11==            N-SSVAPA----------------------------------------------------
+12==            N-SSVSPA----------------------------------------------------
+13==            LRNKVMPAHPV-------------------------------------------------
+30==            ERSEFVLQNSDHCGKKGHDT----------------------------------------
+31=p            ERSEFVLQNSDHCGKKGHDT----------------------------------------
+29==            ERPEFVLQNADYCRKKGHDS----------------------------------------
+32==            ------------------------------------------------------------
+33=p            ------------------------------------------------------------
+34==            ------------------------------------------------------------
+35=p            ------------------------------------------------------------
+36==            ------------------------------------------------------------
                                                                             
 
-14==            -----------------------------
-15==            -----------------------------
-16==            -----------------------------
-17==            -----------------------------
-18==            -----------------------------
-19==            -----------------------------
-20==            -----------------------------
-21==            -----------------------------
-22==            -----------------------------
-23==            -----------------------------
-24==            -----------------------------
-25==            -----------------------------
-26==            -----------------------------
-27==            PPQ--GAPPQVEAPQGAPPQGVDNQAYQA
-28==            PPPPQGAPPQG-APPAAPPQGVDNQAYQA
-9==             -----------------------------
-10==            -----------------------------
-8=opsin_        -----------------------------
-11==            -----------------------------
-12==            -----------------------------
-1==             -----------------------------
-2==             -----------------------------
-4=p             -----------------------------
-5=p             -----------------------------
-3==             -----------------------------
-6==             -----------------------------
-7==             -----------------------------
-13==            -----------------------------
-30==            -----------------------------
-31=p            -----------------------------
-29==            -----------------------------
-32==            -----------------------------
-33=p            -----------------------------
-34==            -----------------------------
-35=p            -----------------------------
-36==            -----------------------------
-                                             
+14==            ----------------------------------------
+15==            ----------------------------------------
+16==            ----------------------------------------
+17==            ----------------------------------------
+18==            ----------------------------------------
+19==            ----------------------------------------
+20==            ----------------------------------------
+21==            ----------------------------------------
+22==            ----------------------------------------
+23==            ----------------------------------------
+24==            ----------------------------------------
+25==            ----------------------------------------
+26==            ----------------------------------------
+27==            QGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQA
+28==            QGYPPQGYPP---PPQGAPPQ-GAPPAAPPQGVDNQAYQA
+1==             ----------------------------------------
+2==             ----------------------------------------
+4=p             ----------------------------------------
+5=p             ----------------------------------------
+3==             ----------------------------------------
+6==             ----------------------------------------
+7==             ----------------------------------------
+9==             ----------------------------------------
+10==            ----------------------------------------
+8=opsin_        ----------------------------------------
+11==            ----------------------------------------
+12==            ----------------------------------------
+13==            ----------------------------------------
+30==            ----------------------------------------
+31=p            ----------------------------------------
+29==            ----------------------------------------
+32==            ----------------------------------------
+33=p            ----------------------------------------
+34==            ----------------------------------------
+35=p            ----------------------------------------
+36==            ----------------------------------------
+                                                        
diff --git a/tools/clustalw/test-data/rgClustal_testout03.dnd b/tools/clustalw/test-data/rgClustal_testout03.dnd
index 1b1dd71db..c24eb8f4b 100644
--- a/tools/clustalw/test-data/rgClustal_testout03.dnd
+++ b/tools/clustalw/test-data/rgClustal_testout03.dnd
@@ -3,101 +3,101 @@
 (
 (
 (
-1==:0.10508,
-2==:0.11044)
-:0.03328,
+1==:0.10466,
+2==:0.11086)
+:0.03287,
 (
-3==:0.10212,
+3==:0.11257,
 (
-4=p:0.03956,
-5=p:0.04640)
-:0.07123)
-:0.03527)
-:0.12883,
-6==:0.25691)
-:0.03351,
-7==:0.25261)
-:0.01354,
+4=p:0.04128,
+5=p:0.04468)
+:0.06078)
+:0.02995)
+:0.11829,
+6==:0.25773)
+:0.01821,
+7==:0.26433)
+:0.02576,
 (
 (
 (
-8=opsin_:0.00232,
+8=opsin_:0.00127,
 (
-9==:0.01369,
-10==:0.02751)
-:0.00485)
-:0.08347,
+9==:0.01804,
+10==:0.02316)
+:0.00590)
+:0.08153,
 (
-11==:0.07845,
-12==:0.09558)
-:0.02853)
-:0.20130,
+11==:0.08862,
+12==:0.08818)
+:0.02496)
+:0.17382,
+13==:0.26257)
+:0.01165,
 (
 (
 (
 (
 (
-14==:0.03776,
-15==:0.05125)
-:0.12161,
+14==:0.04296,
+15==:0.04604)
+:0.10934,
 (
-16==:0.05295,
-17==:0.05551)
-:0.09431)
-:0.20019,
+16==:0.02950,
+17==:0.02077)
+:0.12646)
+:0.18931,
 (
 (
-18==:0.12284,
-19==:0.12385)
-:0.20199,
+18==:0.12161,
+19==:0.12507)
+:0.17514,
 (
 (
 (
 (
 (
-20==:0.02082,
-21==:-0.01799)
-:0.02913,
-22==:0.01073)
-:0.15908,
+20==:0.00751,
+21==:-0.00467)
+:0.02248,
+22==:0.01604)
+:0.14593,
 (
-23==:0.03644,
-24==:0.05280)
-:0.11950)
-:0.05528,
-25==:0.22127)
-:0.02122,
-26==:0.23721)
-:0.07307)
-:0.02400)
-:0.03308,
+23==:0.04207,
+24==:0.04717)
+:0.13371)
+:0.04590,
+25==:0.22090)
+:0.02731,
+26==:0.23656)
+:0.06585)
+:0.00454)
+:0.02246,
 (
-27==:0.14728,
-28==:0.12727)
-:0.26343)
-:0.04564,
+27==:0.12163,
+28==:0.12167)
+:0.20854)
+:0.05872,
 (
 (
-29==:0.02761,
+29==:0.02733,
 (
-30==:0.00213,
-31=p:0.00282)
-:0.02437)
-:0.38262,
+30==:0.00316,
+31=p:0.00179)
+:0.02465)
+:0.31664,
 (
 (
-32==:0.04954,
-33=p:0.05235)
-:0.33117,
+32==:0.05101,
+33=p:0.05088)
+:0.26674,
 (
 (
 34==:0.00000,
 35=p:0.00000)
-:0.33155,
-36==:0.33885)
-:0.04452)
-:0.02854)
-:0.07289)
-:0.12569)
-:0.01983,
-13==:0.31664);
+:0.29806,
+36==:0.30732)
+:0.00817)
+:0.04982)
+:0.08204)
+:0.08853);