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?
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.
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.
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