2026-10-13 https://api.researchdata.se/oai-pmh

oai:researchdata.se:doi-10-17045-sthlmuni-7642463/0 2019-01-29 subject:ssif:10203 subject:ssif:102 subject:ssif:1 subject:ssif:10610 subject:ssif:106 subject:ssif:10615 subject:ssif:10408 subject:ssif:104 principal:slug:stockholm-university

info:eu-repo/semantics/other http://purl.org/dc/dcmitype/Dataset https://doi.org/10.17045/STHLMUNI.7642463 dN/dS calculation of Thermus virus NrdJm evolution https://orcid.org/0000-0002-8779-6464 Christoph Loderer Karin Holmfeldt Bioinformatics (Computational Biology) Bioinformatik (beräkningsbiologi) Bioinformatics and Computational Biology Bioinformatik och beräkningsbiologi Evolutionary Biology Evolutionsbiologi Biochemistry Biokemi A log ratio test of significant overrepresentation of non-synonymous to silent (dN/dS) was estimated with codonml from PAML (Yang 1997, https://doi.org/10.1093/bioinformatics/13.5.555 ; Yang 2007, https://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 https://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. https://creativecommons.org/licenses/by/4.0/ Stockholm University Stockholms universitet 2019-01-29T00:00:00Z