First off, Happy Thanksgiving to the Biostars community! I've been working in PAML to generate a single dn/ds (or, omega) value for an alignment of 16 sequences. However, despite everything I try, I cannot get a single estimate of omega for the alignment in the output file. What I end up getting looks like this:
CI_8_D1 0.0565 (0.0089 0.1581)
CI_9_D1 0.1516 (0.0024 0.0160) 0.0533 (0.0081 0.1521)
Each time I run Codeml, even with aligned sequences for a different protein using a different tree, I also get the following output in the terminal (not the output file itself):
"Seq #1 (CI_7_D1) is missing in the tree." (CI_7_D1 is the name of the first sequence).
The thing is, it isn't missing from the tree. The following is the first line from my .nwk file:
The following is the relevant input for my Codeml ctl file:
runmode = 0, seqtype = 1, CodonFreq = 2, model = 0, NSsites = 0
fix_kappa = 0, kappa = 1, fix_omega = 0, omega = 1, ncatG = 10
Can anyone tell me what the potential issue may be here? I've honestly tried exhausting every resource that I could find online, but it seems that my type of problem isn't one that has been presented to the PAML support community. Any and all help would be greatly appreciated.