Hello,

I'm used to doing smaller multiple sequence alignments (MSA) for 10-20 at once .fasta or .faa files, however I have over 100 files stored in the same directory, is there a specific command to do a MSA for all my files present in the same directory? Below I put an example of something I was trying to do but I want an all vs all alignment, not individually. Preferably with mafft or clustalw :)

Thanks in advanced

for i in *.faa; do mafft --quiet $i > ${i%..faa}.aligned.faa; done