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HyPhy vs. PAML (Read 3175 times)
adk
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HyPhy vs. PAML
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
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Sergei
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Re: HyPhy vs. PAML
Reply #1 - May 10th, 2005 at 1:19pm
 
Dear Andy,

Quote:
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
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Re: HyPhy vs. PAML
Reply #2 - 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
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adk
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Re: HyPhy vs. PAML
Reply #3 - May 10th, 2005 at 2:37pm
 
Great Sergei! Where can I find out the details of how HyPhy deals wiwth ambiguous sites?

cheers,
Andy
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Re: HyPhy vs. PAML
Reply #4 - May 10th, 2005 at 2:46pm
 
Dear Andy,

Quote:
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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Division of Biomedical Informatics
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