Question: CONVERT .aln file to .phy for RAxML input
gravatar for Fid_o
8 months ago by
Fid_o20 wrote:

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?

alignment • 565 views
ADD COMMENTlink modified 8 months ago by Mensur Dlakic7.2k • written 8 months ago by Fid_o20

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.

ADD REPLYlink written 8 months ago by Joe18k
gravatar for Mensur Dlakic
8 months ago by
Mensur Dlakic7.2k
Mensur Dlakic7.2k wrote:

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.

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

ADD COMMENTlink written 8 months ago by Mensur Dlakic7.2k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2231 users visited in the last hour