I have two groups of sequences in separate files (1.fasta and 2.fasta). I need to make comparison between them. However I cannot run
bl2seq -i 1.fa -j 2.fa -p blastp -o output
because bl2seq is expecting only one sequence in a fasta file.
Is splitting multi fasta files the only option to compare each sequence in 1.fa with each sequence in 2.fa?
Thanks for help