Converting Fasta to Phylip sequences sequences must be the same length

Question

[scholz.stacy]

I'm an undergrad student looking for a free software program that will allow me to make my fasta sequences the same length in order to input into Phylip. Is there such a program?

Answer 1

[Michael]

Edit: The sequences you convert to Phylip format have the same length, because they result from a multiple sequence alignment. Check this site for questions related to "Multiple sequence alignment", or Muscle, ClustalW, MAFFT, etc. Or use one of the web-apps: https://www.ebi.ac.uk/Tools/msa/

EMBOSS' seqret program will do the conversion to phylip if required. Here is the EMBL-EBI web server, which most likely will be sufficient for your aim. Note that Phylip format shortens your sequence identifiers brutally, so you might want to avoid it or shorten your identifiers before conversion.

[GenoMax]

Good point. As I recall phylip needs 10 character names so make sure they are unique in that part of the name.

[Michael]

One approach is to number the seq TAX1..N and replace the placeholders in the tree after that with the original data.

Also, the emboss seqret converter has a bug in that output misses a space delimiter between identifier and sequence in phylip format in some cases.