Labeling of foreground branches

[Nina Ramos]

Hi all, 

I have come conducted an analysis comparing the branch models (M0 and M2) and the branch-site models (MA and MA null) to identify differences between the foreground and background. However, I am unsure of the restrictions regarding how many branches you can label as the foreground within each of these comparisons as I have seen some contradicting instructions across the web. One says that the branch-site models can test for episodic selection in two or more foreground branches while others say that only one can be compared and I am uncertain about this for the branch-model as well. 

Codeml allowed me to run both of these analysis to completion with the input of multiple branches as the foreground. Is this still a valid approach or result within the output? Any input on this issue is greatly appreciated. Thank you! 

[Ziheng]

yes, under both the branch and branch-site models, multiple branches can be labeled the forground branches.  the default branch label is #0, which is for the background, while the foreground branches are labeled #1, and multiple branches can be labeled #1.

under the branch-site model, only those two branch labels are allowed: some branches are labeled #1 while the others are unlabeled (which is the same as havaing the label #0).  all branches having the same label #1 are assumed to be under the same seletive regime, with the same proportions of sites having different w ratios (w0, w1, w2).

under the branch model, there can be more than two labels.  for example some branches may have #0 (the default), some have #1, some have #2, etc., and the program will fit w0, w1, w2, ... to them, respectively.  the branches having the same label will have the same w ratio.  for example, all branches labeled #2 will have w2.

best wishes, ziheng