I need to run a program using 2 files as input expecting 1 output having 6000 files ranging from abc0000.faa/abc0000.fna to abc6000.faa/abc6000.fna. I also need the output file to have the same file name as the inputs but .paml extension.
This is an example of the full command just for files 0000.
./pal2nal.pl abc0000.faa abc0000.fna -codontable 11 -output paml > abc0000.paml
Is there a way of running the same command for all files automatically? Something like a for-in-do?