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dNdS (Read 2750 times)

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dNdS
Feb 16^th, 2009 at 8:05pm

Dear Sergei,
I am sorry for disturbing you. I would like to use Hyphy to do dndS analysis and then study the tree branches. I can do at the console:

open data-> select all--> data partition--> codon model + tree + substitution model + local --> build and optimize.

But I have more than 10000 gene families, I would like to do this inside script, just like Tutorial/bfs/basics.bf. Thus, how can I do analysis via script using for example just an MG94*HKY85 model?
Can you give me an example like Tutorial/bfs/basics.bf?

Thank you very much.
,
Bo Li

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: dNdS Reply #1 - Feb 16^th, 2009 at 10:43pm Dear Bo Li, You may find this post useful: Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to Login Best, Sergei
Back to top	Associate Professor Division of Infectious Diseases Division of Biomedical Informatics School of Medicine University of California San Diego WWW IP Logged

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Re: dNdS codons.bf
Reply #2 - Feb 17^th, 2009 at 5:10pm

Dear Sergei,

Thanks so much for your help! GenomeFitters can get globe omega, I would like to change it to get local omega and then study the tree branches.

Thanks for your help! I have another problem:
GettingStarted.pdf explains the file of "codons.bf" (P53), but I can not find it in the package. Could you help me to find the file?

Your help would be greatly appreciated!!

Best,
Bo

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Re: dNdS
Reply #3 - Feb 18^th, 2009 at 7:05am

Dear Bo,

Take a look at Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

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of dN/dS analyses in HyPhy. Some of the supporting batch files are in
Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

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Of particular interest to you may be these two files:

Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

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blue YaBB Newbies Offline Feed your monkey! Posts: 3	Re: dNdS Reply #4 - Feb 19^th, 2009 at 1:23am Dear Sergei, Thanks so much for your help! I would read all carefully. Thanks. Best, Bo
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