I want to apply the following command to all the files in the current directory
clustalw -align -infile=*here goes the input filename* -outfile=*here goes the output filename*
I also want the output filename to be the same as the input plus ".aln". For example:
clustalw -align -infile=nexus0000.fna -outfile=nexus000.fna.aln
Thanks for the help!