I have two questions about codeml of PAML, and i m appreciate for your time to answer my question.
1. How to transfer fasta format into phylip format? And why the length of sequence is same?
Usually i could got a fasta format results after the MSA, and i transfered it into phylip format using DMABE software. However, i always get an error that more space are required behind the sequence name. Then i want to transfer it manually, and i find that the sequence in samples of paml (lysozymeLarge.nuc) are same length. What should i do to deal with my not the same length MSA results? Ps: it seems fine to run codeml with a fasta format sequence, could anybody tell me what the impact will have in my results of codeml with fasta sequence?
2. Branch labels
I had read the manual of PAML, and i still confused about the # and $. For example, supposed that i have a gene tree that there are 'A' and 'B' gene with 5 species, respectively, and i want to test dn/ds of 'A' gene in these 5 species. Should i label #1 or $1 to the ancestral sequence of these species? #1 means only label the ancestral sequence, whilst $1 means label all 'A' genes. Which one label is right?
Thanks for your time!