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HYPHY Package >> HyPhy feedback >> IFEL LTR http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1150888730 Message started by YER on Jun 21st, 2006 at 4:18am |
Title: IFEL LTR Post by YER on Jun 21st, 2006 at 4:18am
Dear Sergei,
I am trying to dive into the population-based analyses of dN/dS ratios based on your paper in PLoS Computational Biology. One thing that is not clear to me is how to implement the test to determine the significance of IFEL test. I have scrolled through the various options that might comprise this test, but was unable to find it. The subtreeselectioncomparison.bf can be used to carry out the IFEL test for individual sites in a sample, but the LRT to assess the significance of any temporal heterogeneity of dN/dS across sites in a population sample does not seem to be in the standard options of HYPHY. Is this correct? If so, could you point out how to set up this LRT and especially how to assign tips, interiors, and the two site classes? Thanks again, Yer |
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