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HYPHY Package >> HyPhy feedback >> HyPhy vs. PAML
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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:
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?


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

Title: Re: HyPhy vs. PAML
Post by Sergei on May 10th, 2005 at 2:46pm
Dear Andy,


wrote 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


Pages 5-6 of Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login. Also, HyPhy includes ambiguities when counting base frequencies (by allocating 1/k count to each possible resolution).

Cheers,
Sergei

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