I have 2 sets of 6000+ files ( protein and nucleotide) representing each family from 15 different strains. Next i intend to use pal2nal to achieve codon alignment however the order are not identical. This is crucial in order to execute loop for each files.
./pal2nal.pl protein_group1.fasta nuc_group1.fasta -output paml > result_group1.paml
but instead the correct match is
protein_group1.fasta - > nuc_group57.fasta
protein_group2.fasta - > nuc_group327.fasta
and so on ...
I was able to check the corresponding files by manually tagging using the grep command hence, it would be slow and impractical. How can i solve this problem ?