Directory rather than a single file as an input?

[neginmb]

How to provide cd-hit with a directory rather than a file as input? My purpose is to compare all the sequences in all fasta files in this directory against each other and cluster them.

[acvill]

My purpose is to compare all the sequences in all fasta files in this directory against each other and cluster them.

Concatenate the individual files, then run cd-hit on the concatenated file.

cat dir/*.faa > all.faa cd-hit -i all.faa -o clustered.faa