publication . Preprint . Article . 2017

Calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates

Sydykova, Dariya K.; Wilke, Claus O;
Open Access
  • Published: 01 May 2017
  • Publisher: PeerJ
Abstract
<jats:p>Site-specific evolutionary rates can be estimated from codon sequences or from amino-acid sequences. For codon sequences, the most popular methods use some variation of the <jats:italic>dN</jats:italic>∕<jats:italic>dS</jats:italic> ratio. For amino-acid sequences, one widely-used method is called Rate4Site, and it assigns a relative conservation score to each site in an alignment. How site-wise <jats:italic>dN</jats:italic>∕<jats:italic>dS</jats:italic> values relate to Rate4Site scores is not known. Here we elucidate the relationship between these two rate measurements. We simulate sequences with known <jats:italic>dN</jats:italic>∕<jats:italic>dS</jat...
Subjects
free text keywords: Evolutionary biology, Statistical inference, Correlation, Biology, Divergence, Sequence analysis, Evolutionary rate, Codon evolution models, Amino-acid evolution models, Rate variation, Medicine, R, Bioinformatics, Computational Biology, Evolutionary Studies, Statistics
Funded by
NIH| The biophysical basis of translational selection
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM088344-03
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
NSF| BEACON: An NSF Center for the Study of Evolution in Action
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0939454
  • Funding stream: Directorate for Biological Sciences | Division of Biological Infrastructure
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