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Datamonkey Server >> Datamonkey feedback >> Differences between PAML and DATAMONKEY results http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1145989307 Message started by Denise on Apr 25th, 2006 at 11:21am |
Title: Differences between PAML and DATAMONKEY results Post by Denise on Apr 25th, 2006 at 11:21am
I recently analyzed the same data set using both PAML and Datamonkey and found that the sites identified under positive selection differ between the two completely. Here's the details:
PAML - The LRT between M1 and M2 is not significant while that between M7 and M8 is significant. The estimated omega for M8 is 1.18496 with 0.07359 as the proportion of sites in this category. The BEB found 9 sites positively selected with one site greater than .95. The same data set run through Datamonkey found 3 sites in the FEL and SLAC analyses positively selected at the .05 significance level. Of these sites, two out of the three are the same between the two analyses. These sites do not have any overlap with the PAML analysis (there is no overlap even at the .1 significance level in Datamonkey). And finally, my data set contains 42 species and 294 amino acids. If you need any more information, let me know. So my questions include: Has this happened to other people? Under what conditions might this happen? For example, it appears in this case that sites may be positively selected but not at a level much higher than the neutral rate. Is this a likely factor in conflicting results and is there any other conditions where such conflicts will arise? Why might I get such different results from these two programs? And for the big question: Any suggestions on how these results should be interpreted? Thanks for any help, - Denise |
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