It just occurred to me that targeting a specific lineage for the BS-REL test a priori will not produce different results from running the model on the full dataset (other than saving computational cost and time). So might it be statistically OK to disregard the other lineages and assess the evidence for selection from the LRT and p-value of only my a priori selected lineage (rather than the p_Holm)?

Hi Sergei,

Thanks for the file, that will certainly help and save your datamonkey servers from analyzing my dataset!

I'm curious which case you find more convincing from these two nested BS-REL analysis.

A dataset of 51 mammalian species with 213 codons where BS-REL identifies positive selection in human with mean omega=10, omega1=0.0008 (P1=0.68), omega2=0.0008 (P2=0.56), and omega3=1000 (p3=0.09) at LRT=5.22 and p-value=0.01.

Or dataset of 18 primate species selected from the larger 51 species dataset where BS-REL identifies positive selection in human with mean omega=10, omega1=5E-9 (P1=0.88), omega2=7.5E-8 (P2=0.03), and omega3=1000 (p3=0.085) at LRT=8.7 and p-value=0.0017.

Both are statistically signifiant and have similar results, but should one always prefer a larger dataset (so long as the alignment is clear)?

Thanks,
Vinny