This supplementary data set provides alignment data and alignment visualizations in the individual_results folder. The visualizations show positively selected sites and filtered alignment regions. The folder structure is like this: individual_results/[Gene name]/[Sequence ID]/[alignment and visualization files] The Sequence ID level reflects the circumstance that for many genes multiple splice variants were tested for positive selection. The CDS alignment files are called: prank.best.fas.renamed The corresponding protein aligments are called: prank.best.fas.translation The visualizations are the .view files and can be opened with the script viewer.pl that is in the same folder as this readme. Prerequisite is that Perl and Java are installed. Before you can start to visualize the *.view files via the viewer.pl script you have to download some execuatble files of the actual alignemnt viewer program, Jalview*, that will be used by the viewer.pl script. Unfortunately, the Data Dryad team has forbidden me to directly include these files into this package for licensing reasons. Therefore, execute the folowing command once to automatically download all required executable files: perl viewer.pl -download If this does not work for some reason, you have several alternatives which are discussed at the bottom of this document. After you have executed the above command once or used alternative 1-2 at the end of the document, you can visualize the *.view files as shown in the following example. Example: perl viewer.pl individual_results/TXN/c204079.graph_c0_seq1/prank.best.fas_7.translation.view The above command will open the alignment of thioredoxin (TXN) with Jalview* and highlight the positively selected sites of branch 7 (compare with phylogeny_with_branch_numbers.png in this folder). The file extension "translation.view" means that the visualization is opened on the protein level. The corresponding file prank.best.fas_7.view opens the same alignment on nucleotide level. Alternative ways to get the required executables for alignment visualization: 1) You can download the missing files manually from our group's ftp-server: ftp://genome.leibniz-fli.de/pub/mrps2017/jalview.tar.gz Just unpack, and ensure that the file "jalview.jar" and the folder "lib" lie in the same directory as this readme file. 2) You can download a version of this supplement with all necessary files included: ftp://genome.leibniz-fli.de/pub/mrps2017/supplement_data.tar.gz 3) In case the mentioned ftp-server does not exist anymore, you still should be able to download the software "PosiGene", which can also open the *.view files, from the public software repository github: https://github.com/gengit/PosiGene/archive/v0.1.zip After you have unpacked the software you can open the *.view files in an only slightly different way than mentioned above. Example (equivalent to the above one): perl PosiGene-0.1/PosiGene.pl -view=individual_results/TXN/c204079.graph_c0_seq1/prank.best.fas_7.translation.view ------------------------------------------------------------------------------------------------------------------- *Jalview citation: Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009) "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench" Bioinformatics25 (9) 1189-1191 doi: 10.1093/bioinformatics/btp033