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HYPHY Package >> HyPhy feedback >> Codon-based selection analysis for homologous sequences and GARD http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1347680919 Message started by Jack wong on Sep 14th, 2012 at 8:48pm |
Title: Codon-based selection analysis for homologous sequences and GARD Post by Jack wong on Sep 14th, 2012 at 8:48pm
Hi,
I am new to the forum and also new to use the selection methods so have some basic question regarding analysis. Would be pleased to have opinion and suggestions! 1. Is codon based analysis suitable for within species(homologous genes) selection analysis? The reason being high recombination within the population? 2.I used GARD method and the program gave me one potential break-point with High AIC score with exact location. However, the program out put read like this "The alignment contained 85 potential breakpoints, translating into the search space of 3655 models with up to 2 breakpoints of which 79.15% was explored by the genetic algorithm". Bit confused now how does 85 potential breakpoints leads ultimately to one. :D 3.For a particular codon, selection analysis using GARD inferred tree I could only get positive selection from two methods REL(Bayes factor 190.59) and FUBAR(posterior probabbility 0.915). How reliable are these two significance values? Thank you in advance! :) Jack |
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