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FEL question (Read 2439 times)

Antonio

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FEL question
Mar 12^th, 2008 at 7:17am

Dear Sergei, I am performing a FEL analysis in the server. I am also performing a codon analysis in my computer using dNdSrateanalysis.bf. I am getting very different results concerning the number of selective sites detected. In the .bf I am using MG94 with nonsynonymous rate model and getting a lot of positive sites both with 3x3 or 3x4 rates and general discrete distribution.
I am wondering how I can perform in my computer the corresponding FEL I am doig in datamonkey?

thank you very much,

Antonio

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Sergei

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Re: FEL question
Reply #1 - Mar 12^th, 2008 at 10:06am

Dear Antonio,

REL (dNdSRateAnalysis.bf) can give you a lot of 'iffy' positive results for small alignments, especially if the model is complex.
Treat them with caution, e.g. run them through SLAC and look at the relative numbers of syn and non-syn substitutions at a site
as a sanity check.

To run FEL on your machine, follow the instructions of section 2.6.4 in Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

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Antonio YaBB Newbies Offline I love YaBB 1G - SP1! Posts: 15	Re: FEL question Reply #2 - Mar 12^th, 2008 at 4:29pm Thank you very much! I get now the same results , Antonio
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