dN/dS calculation of Thermus virus NrdJm evolution

A log ratio test of significant overrepresentation of non-synonymous to silent (dN/dS) was estimated with codonml from PAML (Yang 1997, doi.org/10.1093/bioinformatics/13.5.555 ; Yang 2007, doi.org/10.1093/molbev/msm088) by running the program with a fixed and free dN/dS respectively, and the branch leading to the two Thermus virus sequences (marked with “#1” in reftree.newick) designated as the “foreground” branch in the free dN/dS run.

This analysis was performed on the Thermus virus/Firmicutes subtree in doi.org/10.17045/sthlmuni.7117430.v2, using the same alignment as for the full tree, reverse translated into nucleotides. We could not find correct gene sequences for seven taxa (RefSeq accession numbers: WP_102410887, WP_033167051, WP_054955013, WP_065068364, WP_088370373, WP_087372021, WP_093315575), so they were left out of the analysis. Scripts in files ending with .codeml; output in .codeml.out files.