dN/dS calculation of Thermus virus NrdJm evolution
Description
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.
Resources
| Name |
Format |
Description |
Link |
|
0 |
|
http://data.europa.eu/88u/dataset/https-doi-org-10-17045-sthlmuni-7642463 |
Tags
- 60102-bioinformatics
- biochemistry
- computational-biology
- dataset
- evolutionary-biology
- 60309-phylogeny-and-comparative-analysis