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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl Methodology Questions >> How to >> dNdS http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1234843540 Message started by blue on Feb 16^th, 2009 at 8:05pm

Title: dNdS
Post by blue on 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

Title: Re: dNdS
Post by Sergei on 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

Title: Re: dNdS codons.bf
Post by blue on 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

Title: Re: dNdS
Post by Sergei on 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

Title: Re: dNdS
Post by blue on Feb 19^th, 2009 at 1:23am

Dear Sergei,

Thanks so much for your help! I would read all carefully. Thanks.

Best,
Bo