CONVERT .aln file to .phy for RAxML input
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?
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Mensur Dlakic
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Fid_o •
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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.
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When you say you have a file with a
.alnsuffix, exactly what format is the alignment? File extensions are only convention in*nixoperating systems, they don't actually define what the file is.Please show us some of the input data.