From 59718087b5423bf679857a1355bb32a2f05e3afa Mon Sep 17 00:00:00 2001
From: Siavash Mirarab <smirarab@gmail.com>
Date: Mon, 11 Jul 2016 18:20:24 -0700
Subject: [PATCH] Version 4.10.7

---
 CHANGELOG.md                                | 3 ++-
 main/phylonet/coalescent/CommandLine.java   | 4 ++++
 main/phylonet/coalescent/SpeciesMapper.java | 3 +++
 main/phylonet/coalescent/WQInference.java   | 9 +++++++++
 4 files changed, 18 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9cd50c2b9..54939149d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,7 @@
 - version 4.10.7:
-	- Small bug fix: with `-a` scoring using `-q` didn't work 
+	- Small bug fix: with `-a` scoring using `-q` didn't work. Also, output both gene tree labels and the species tree labels. 
 	- Bug fix: effective N and quartet scores were not correctly printed out with -t X options if gene trees had polytomies. posterior values were correctly computed.
+	- Warning for low `EN` values.
 	- Some spell checking on prompts
 	
 - version 4.10.6:
diff --git a/main/phylonet/coalescent/CommandLine.java b/main/phylonet/coalescent/CommandLine.java
index c5b9f9dca..ed7ac90f4 100644
--- a/main/phylonet/coalescent/CommandLine.java
+++ b/main/phylonet/coalescent/CommandLine.java
@@ -383,6 +383,10 @@ public static void main(String[] args) throws Exception{
 					bestTree.add(tr);
 				}
 				
+				if (!GlobalMaps.taxonNameMap.getSpeciesIdMapper().isSingleIndividual()) {
+					System.err.println("Scored tree with gene names:\n"+tr.toNewickWD());
+				}
+				
 				GlobalMaps.taxonNameMap.getSpeciesIdMapper().gtToSt((MutableTree) tr);
 				
 				if (options.getBranchannotation() != 12) {
diff --git a/main/phylonet/coalescent/SpeciesMapper.java b/main/phylonet/coalescent/SpeciesMapper.java
index e604f0b79..469ffe407 100644
--- a/main/phylonet/coalescent/SpeciesMapper.java
+++ b/main/phylonet/coalescent/SpeciesMapper.java
@@ -235,4 +235,7 @@ public void gtToSt(MutableTree st) {
     	}
     }
 
+    public boolean isSingleIndividual() {
+    	return taxonIdToSpeciesId.length == speciesIdtoTaxonId.size();
+    }
 }
\ No newline at end of file
diff --git a/main/phylonet/coalescent/WQInference.java b/main/phylonet/coalescent/WQInference.java
index b80cfa606..9ff1584ce 100644
--- a/main/phylonet/coalescent/WQInference.java
+++ b/main/phylonet/coalescent/WQInference.java
@@ -226,6 +226,15 @@ public double scoreBranches(Tree st) {
 				nd.mainfreq = s.qs;
 				nd.effn = s.effn;
 				
+				
+				if (nd.effn < 20) {
+					if (!GlobalMaps.taxonNameMap.getSpeciesIdMapper().isSingleSP(cluster.getBitSet()))
+						System.err.println("You may want to ignore posterior probabilities and other statistics related to the following "
+								+ "branch branch because the effective number of genes impacting it is only "+ nd.effn +
+							". h:\n\t" +
+							GlobalMaps.taxonNameMap.getSpeciesIdMapper().getSTClusterForGeneCluster(cluster));
+				}
+				
 				Quadrapartition[] threequads = new Quadrapartition [] {quad, null,null};
 				
 				quad = weightCalculator2.new Quadrapartition