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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl Theoretical questions >> Sequence Analysis >> ASR http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1305051414 Message started by Kartik Sunagar on May 10^th, 2011 at 11:16am

Title: ASR
Post by Kartik Sunagar on May 10^th, 2011 at 11:16am

Dear all,

I am new to this. I am using the ASR algorithm to reconstruct ancestral sequences. I wanted to know, out of the three types of sequences generated by the program (marginal, joint and sampled), which is the most reliable one? Does this solely depend on the support values for each type? Can I rely on these sequences to evaluate the selection regimes for the particular clade the sequence represents?

Thank you very much,
Kartik

Title: Re: ASR
Post by Sergei on May 11^th, 2011 at 11:23am

Hi Kartik,

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

Login for some discussion. You should NOT use ancestral sequences to infer anything about selection -- there are dedicated methods for doing that (SLAC/FEL/REL etc).

Sergei

Title: Re: ASR
Post by Kartik Sunagar on May 11^th, 2011 at 2:02pm

Dear Sir,

Thank you very much for the reply.

What I meant was, I wanted to construct a homology model for the ancestral sequences and infer the sites/domains under selection so that I could compare it with the extant proteins. Is that inappropriate?

Thank you very much,
Kartik :)

Title: Re: ASR
Post by Sergei on May 12^th, 2011 at 1:08pm

Hi Kartik,

Sure, for simply mapping which substitutions happened along which lineages, ASR is fine (use the joint mode for that).

Sergei

Title: Re: ASR
Post by Kartik Sunagar on May 13^th, 2011 at 2:14pm

Thank you for the help.

Best,
Kartik