I am trying to automate pal2nal but I am struggling to understand.
I have many nucleotide and protein alignment files with the same names and different extensions. For example:
I can run pal2nal by:
pal2nal.pl file1.msa file1.fa -output paml > file1.cds
I need to create a for loop to do this to hundreds of files. How do I do this when the extension changes for the 2 input files and for the output file?