CONVERT .aln file to .phy for RAxML input

Question

[Fid_o]

I ran roary on sequences and I have an aligned file with the extension .aln. I would like to run this aligned file on RAxML which needs a .phy file. How do I convert .aln file to sequential .phy?

[Joe]

When you say you have a file with a .aln suffix, exactly what format is the alignment? File extensions are only convention in *nix operating systems, they don't actually define what the file is.

Please show us some of the input data.

Answer 1

[Mensur Dlakic]

One program that can do this is trimAl, which also happens to trim multiple alignments as a step before building phylogenetic trees. The option you will need is -phylip, and you can do the conversion without trimming.

http://trimal.cgenomics.org/use_of_the_command_line_trimal_v1.2

I am certain there are other programs to do this since alignment conversion is a common task, so you may want to consult Google.