HyPhy message board | |
http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl
HYPHY Package >> HyPhy feedback >> HyPhy vs. PAML http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1115756251 Message started by adk on May 10th, 2005 at 1:17pm |
Title: HyPhy vs. PAML Post by adk on May 10th, 2005 at 1:17pm
Hey Guys,
So here's a question: I've been comparing some output from HyPhy to PAML output, and for some reason things look very different. In particular it seems like branch lengths are very often shorter in HyPhy than in PAML. To bench mark this I have been using the default (model = 0) settings of GY94 (in HyPhy) to PAML codeml output. I'm using the post_dNdS.bf file to parse branch lengths btw. Any insights? cheers, Andy |
Title: Re: HyPhy vs. PAML Post by Sergei on May 10th, 2005 at 1:19pm
Dear Andy,
wrote on May 10th, 2005 at 1:17pm:
Could you send me the benchmark file and codeml output, so that I can see what's going on? I am guessing this is a scaling issue... Cheers, Sergei |
Title: Re: HyPhy vs. PAML Post by Sergei on May 10th, 2005 at 2:27pm
Dear Andy,
I looked at your example, and it is indeed a scaling issue. PAML output looks like Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). tree length = 0.50537 (1: 0.097822, 2: 0.095322, 3: 0.312227); (mel: 0.097822, sim: 0.095322, yak: 0.312227); HyPhy reports (mel:0.0307338,sim:0.0327225,yak:0.100553). Effectively HyPhy branch lengths (substitutions per nucleotide site) are 1/3 of what PAML reports (substitutions per codon) site. Other subtle difference could arise because HyPhy and PAML treat ambiguity data a bit differently as I recall. Cheers, Sergei |
Title: Re: HyPhy vs. PAML Post by adk on May 10th, 2005 at 2:37pm
Great Sergei! Where can I find out the details of how HyPhy deals wiwth ambiguous sites?
cheers, Andy |
HyPhy message board » Powered by YaBB 2.5.2! YaBB Forum Software © 2000-2024. All Rights Reserved. |