jxn
YaBB Newbies
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I love YaBB 1G - SP1!
Posts: 10
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Hi,
I worked on HyPhy and PAUP with same data, tree topology, and model (GTR). They gave very closed branch length for the tree but very different Log likelihood(-3594 from Hyphy, -3815 from PAUP).
Any reasons for this different result? Thanks.
my HyPhy code:
DataSet myData = ReadDataFile Hominoid.txt"); DataSetFilter myFilter = CreateFilter (myData,1);
HarvestFrequencies (obsFreqs, myFilter, 1, 1, 1); REVRateMatrix = {{*,a,b,c}{a,*,d,e}{b,d,*,f}{c,e,f,*}}; Model REV = (REVRateMatrix, obsFreqs); Tree myTree = ((((((Ch,Bo),Gr),Hm),Or),Gb),Mc);
LikelihoodFunction theLikFun = (myFilter, myTree, obsFreqs); Optimize (paramValues, theLikFun); fprintf (out.txt, theLikFun);
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