HyPhy message board | |
http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl
Methodology Questions >> How to >> Generate synrate or nonsynrate tree http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1101838973 Message started by Jeff Mower on Nov 30th, 2004 at 10:22am |
Title: Generate synrate or nonsynrate tree Post by Jeff Mower on Nov 30th, 2004 at 10:22am
After codon based ML analyses, hyphy reports a total branch length tree in parenthetical tree format. Is there any way to take the estimated synrates or nonsynrates and report them in the same tree format?
Thanks for your help. Jeff |
Title: Re: Generate synrate or nonsynrate tree Post by Sergei on Dec 1st, 2004 at 2:15am
Dear Jeff,
Presuming you have used a model which fits different syn and non-syn rates (local models), you can use the tree viewer to scale the tree on syn rates or non-syn rates and write it out a Newick string. Open Object Inspector (Window Menu), display the list of trees in memory (the ones involved in likelihood functions will be in bold), double click on the one you want to display. Once the tree viewer has opened, you can an appropriate 'Branch Scaling' and then invoke 'File->Save'. Note that this will scale the tree on rates, NOT on expected syn subs or non-syn subs. The latter can also be done, but differently. HTH, Sergei |
Title: Re: Generate synrate or nonsynrate tree Post by Leslie Turner on Dec 20th, 2004 at 11:59am
Dear Sergei:
I'd like to produce a tree scaled by expected number of synonymous substitutions, how would I do that? I also noticed that if I scale by syn rate (or exp subst or nonsyn rate) then hit the button again the branch lengths sometimes change substantially- are the rates re-estimated each time? Thanks a lot! Leslie |
HyPhy message board » Powered by YaBB 2.5.2! YaBB Forum Software © 2000-2024. All Rights Reserved. |