I have a file with 132 sequences, across 22 species and want to use baseml to estimate branch lengths. My question is when making the tree file in newick format, how do I account for multiple samples within different species? Would I need to have the sequences for each species named identically in the sequence file so that they can be matched to the tree file? I am completely new to PAML and understand this may be a basic question, so thank you for your patience ahead of time.

P.S. There are uneven sample sizes if this makes a difference, and there is a small amount of within species variation.