phylociraptor v0.9.7

Changes since last release:
0017e9e Bump version to 0.9.7
8aa7a12 phylociraptor: Fix raxml tree path searching for util
25e5490 plot-tree.R: Fix color generation for < 11 colors)
1f09208 estimate_conflict.py: Code cleanup, add warning when nquartets exceeds total number of possible quartets. Adjust similarity calculation accordingly
543da3e Add missing muscle_parameters in config files of test cases
c7629f9 Update README with util information.
1c57aae Rename flag to specify quartets
eaa8cb0 Code cleanup for plot-tree
b24b8af Improvements for usage information of phylociraptor util
e059c57 Update documentation to include information about phylociraptor util
36e20c2 Extend plot similarity functionality. Now tip2tip distances of trees can be calculated and plotted as PCA
604cb2d Update .gitignore
39d0af2 Refine script. Add possibility to have detailed tree information
16b3965 Add additional usage info
ffd7850 Add help for new plot-similarity util
390c53e Add new util plot-similarity to plot a similarity matrix of quartet differences and prepare for PCA plotting
40e63c1 Remove printing of docker command
607db73 Add R scripts used in phylociraptor util
4d4552c phylocriptor docker now by default updates its image as singularity images are pulled inside of it
f3fefb7 update gitignore
3f65b22 Create phylociraptor_modules to as part of cleaning up code in phylociraptor script. Rename compare_tree.py script
4c11e36 phylociraptor: add wd bindpoint to util calls to prevent singularity problems with phylociraptor-docker on Macs
fbb5fab util: Fix small bug compare_tree.py which lead to trees not being counted correctly
b4b8e14 phylociraptor: make compare-trees available in util
eb4e9f2 Add compare_trees script to util
4f5484c Add phylociraptor util and first module for downloading lineage information
b9b4ae4 report: If random seed is set, use this information also in the report-figure to get consistent colors
b87875a mltree: Separate iqtree from preparing iqtree input. This is now done in a new rule prepare_iqtree
16e79fa Update Documentation
6eb4f4e align: Add support for MUSCLE aligner
47e4295 report/filter-align: Fix small bug causing the filtered alignments table to be messed up in the report.
7a4d5e4 More informative rulenames and cleaned up cluster config files
7804d03 Make parsing of config file parameters with different options easier: Now strings (seperated by space and comma) as well as python lists are accepted
846a7aa report: Fix small error in commandline parsing of report figure
7767fda report: Make sure parsimony informative sites information is taken directly from config.yaml
c3f5d0f Correct typo also in config files for test cases following PR #21
56c9681 capture log / stderr during alignment
82daca2 change input function to return gene id instead of path; don't use 'bc'
963a73f make sure working directory for aliscore is removed if it happens to exist from previous aborted run
bca8039 change input files so that mltree mode only reruns individual combinations rather all in case modeltest is partly rerun
6b18418 fix typo