dN/dS calculation of Thermus virus NrdJm evolution
type: Dataset
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.
creative work status: completed
  type: DefinedTerm
  in defined term set: http://publications.europa.eu/resource/authority/dataset-status
  term code: COMPLETED
creator: Daniel Lundin
creator: Christoph Loderer
creator: Karin Holmfeldt
date modified: 2019-01-29
date published: 2019-01-29
keywords: Bioinformatics (Computational Biology)
  type: DefinedTerm
  term code: 10203
keywords: Bioinformatics and Computational Biology
  type: DefinedTerm
  term code: 10610
keywords: Evolutionary Biology
  type: DefinedTerm
  term code: 10615
keywords: Biochemistry
  type: DefinedTerm
  term code: 10408
keywords: 60102 Bioinformatics
keywords: Computational Biology
keywords: 60309 Phylogeny and Comparative Analysis
license: https://creativecommons.org/licenses/by/4.0/
publisher: Stockholm University
version: 0

PropertyValue
property ID: DOI
value: 10.17045/STHLMUNI.7642463

Daniel Lundin
type: Person

Stockholm University
type: Organization