I have a set of sequence files with very long names. If I use clustal-omega for MSA, the .fasta format output retains the full sequence name. However, if I create an MSA in .phy (PHYLIP) format, the sequence name is automatically truncated to 10 characters.

I tried to get around this by first creating a .fasta file and then using the Biopython program described here

http://sequenceconversion.bugaco.com/converter/biology/sequences/fasta_to_phylip.php

to convert to .phy, but the conversion program also truncates the filename. Is there a straightforward work-around? The only thing I can think to do is to write a python script to change the sequence names to a short identifier and store a dictionary, but I'd much rather just create .phy files with the full sequence names to begin with.