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methology for selection analysis of alignment with recombination (Read 1920 times)
Russell
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methology for selection analysis of alignment with recombination
Mar 18th, 2014 at 4:03am
 
Dear Dr. Sergei
I have few question, i want to go for codon selection analysis (SLAC,FEL, REL, FUBAR). I have screened with GARD and SBP for recombination.
1. GARD- shows two breakpoint- 1597 and 2482 position, but SBP show one breakpoint -2495 position for same multiple sequence alignment (MSA). Why this discrepancy in result, which one to take.

2. How to correct for recombination- Methology,
        a. whether to download GARD Nexus output file after screening for GARD analysis and upload it in, analyze ur data option in datamonkey , to proceed for (SLAC,FEL, REL, FUBAR) analysis                                                 
                                           ( or ) 
        b. otherwise based on breakpoint position, i have to split all the sequences of alignment, into fragment , then align each fragment section to MSA, upload each fragment section MSA to proceed for analysis in datamonkey server.

3. whether i can use Parris directly on alignment containing recombination, inaddition to above (SLAC,FEL, REL, FUBAR) analysis.

I am novice to datamonkey, selection analysis. Some question may look silly, sorry. Kindly answer my queries.
I have also referred this article Phylogenetics-
Robust inference of positive selection from recombining coding sequences- Konrad Scheffler, Darren P. Martin and Cathal Seoighe.

Thank u
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Russell
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Curious HyPhy user

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Re: methology for selection analysis of alignment with recombination
Reply #1 - Apr 10th, 2014 at 2:10am
 
Dear Dr/Sir/Madam,
kindly reply to my above question, if any one knew the answer.
THANK U
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