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HYPHY Package >> HyPhy feedback >> How to fetch the sequence Ids for recombinant sequences http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1353585254 Message started by RTuteja on Nov 22nd, 2012 at 3:54am |
Title: How to fetch the sequence Ids for recombinant sequences Post by RTuteja on Nov 22nd, 2012 at 3:54am
Hi Sergei,
I got the GARD output for few gene families. But it just reports me whether the breakpoint (with position) is significant or not. Is there any way to fetch the id of the sequences where recombination is detected. I want to discard the sequences that have been detected with recombination to proceed for selection analysis. May be I am missing something while reading the documentation. Can you please help! Thanks, Reetu |
Title: Re: How to fetch the sequence Ids for recombinant sequences Post by RTuteja on Nov 23rd, 2012 at 6:28am
I tried to identify the sequences involved in recombination events using Geneconv. But in few cases, geneconv does not identify any recombination fragments though breakpoint has been reported GARD. Can you please suggest what should I do in such cases.
I do have few gene family with 506 sequences. Does GARD works fine for such a large dataset? |
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