I recently try BEB test in PAML codeML, using the tree as newick format build by phylip like that:
((((pan:0.00874,homosap:0.00475):0.02235,macaca:0.02894):0.10984,
(rat:0.06275,mus:0.05143):0.14990):0.02776,orc:0.09433,
felis:0.12505);
but after setting up the parameter and run the program it shows this:
Error: need branch labels in the tree for the model..
I have no such problem when running NEB test. I don't know what "branch label" require in PAML cause the number in the tree file are the "branch label".
I found this in the ouput result of codeML branch model:
(MUS #0.3455 , RAT #0.4993 , ((MACA #0.7095 , (HOMO #0.5612 , PAN #999.0000 ) #0.4725 ) #0.6792 , (ORCI #0.7937 , FEL #0.4242 ) #0.7803 ) #0.4347 )
and I try to input it as the tree file.. now it prompt:
Species MUS?
It seems still has sth wrong with the tree format
IN PAML, "Species MUS?" means it did not find species named MUS in input sequence alignment.
And for branch label, tree files looks like ((pan#1, homo), macaca) means branch leading to pan is labeled. please read pdf file of PAML document. There is a section about labelling the background branch.
Best.
See page 15 in the PAML manual on branch/ node labeling. You seem to be confusing branch lengths and labels. The ":" notation is for branch lengths, and "#" notation is for branch labeling- for example specifying genus pan as shown in the example Shuo provided.
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