Hello again,
I have run BranchSiteREL.bf on my data above (300 codon positions from 29 sequences aligned in protein space and a maximum likelihood tree from this alignment) and it seems that there was statistical evidence for episodic positive selection in a proportion of sites on two of the branches (one being an outgroup). However I have some questions about the interpretation of the results files and would be very grateful if you could help me with them. Below are some lines of interest (tell me if you need me to attach all the file):
Branch,Mean_dNdS,RateClasses,OmegaOver1,WtOmegaOver1,LRT,p,p_Holm,BranchLength
Outgroup4,0.6338530211413603,2,39.50934283283482,0.05867113793959489,12.57492751
991231,0.0001954782029494062,0.01075130116221734,0.2337171125395624
8,0.7937461041192106,2,513.7712033581857,0.003730739712586084,10.18154377818246,
0.0007092668219026432,0.03830040838274273,0.006621847307589422
25,10,1,950694.3545098663,1,0.6620847626218165,0.2079124535772852,1,0.0011004592
86759653
1) If I understand things correctly this means that, for example for branch 8, the mean dNdS for this branch is around 0.8 but there are a fraction of 0.3% of sites that have a mean dNdS of 513? Why did this branch was identified as significant and branch 25 did not? (is it because the latter was assign with only one omega rate class? despite the much higher omega value?)
2) in the output ps file I see the branch leading to the Outgroup4 as a blue thick line with red in the tip end but for branch 8 I only see a black thick line. Is this ok? shouldn't this branch be colored? or has this to do with the fraction of sites that were identified as being under diversifying selection?
Other more general questions (if I may):
3) I am mainly using intrapopulation data with an introgressed region in one of the populations. Is this ok for this type of analysis?
4) Does BranchSiteREL also tests for a global fitting or this as to be done separately?
Sorry if all these sound like naive questions but I am just now getting into selection analysis.
Thanks.
Pedro