Hi all, I'm using clustalw2:

I know that clustal requires a file to read and it outputs to a file. Is there way I can just supply the sequences as a parameter, for example instead of

clustalw2 input.fasta -OUTPUT=PHYLIP -GAPOPEN=1 -GAPEXT=20

can I just somehow replace the file input.fast with just two sequences instead? And get it to output the resulting alignment without writing to a file. The reason why I would like to do this is because I want to call this program from PERL script and I thus I simply want to provide the input and capture the output.

thanks in advance!

Alex