Comments (2)
Hi,
You can convert an alignment in a3m format to .aln
format using a couple of shell commands; we use this:
$ grep -v '^>' file.a3m | sed -e 's/[a-z]//g' > file.aln
In short, you only have to remove the lines beginning with '>' and delete lowercase characters from the a3m file. In both a3m and aln alignments, the query sequence should be the first sequence.
HTH
from dmpfold2.
Thank you, works excellent!
My .a3m
examples got #
in first line, so I made small modification to have more universal command:
$ sed -e 's/[a-z]//g' file.a3m | grep '^[A-Z\-]' > file.aln
from dmpfold2.
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