How to test evolutionary rates for each species in a gene alignment?
Entering edit mode
4.3 years ago
DNAngel ▴ 240

I was wondering if there are any R packages or tools that can determine the evolutionary rates of species given their tree (with branch lengths) and an alignment file for a specific gene. I want to see if some species belonging to a clade are evolving more quickly than the ancestral clades. Is this possible? I know dN/dS ratios can determine evolutionary rate across the whole file and clade models can asses partitions, but is there a way to get the INDIVIDUAL species evolutionary rate so I can average it myself? Or can I assume that clade models in PAML do this automatically if I put my whole clade as the foreground?

I was thinking something like Pagel's test but that doesn't seem to take into account sequence files...

If you have any ideas or know of an R package/tool that can do this please advice me !

evolutionary rate R • 636 views

Login before adding your answer.

Traffic: 2465 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6