Question: Multiple Sequence Alignment (Same Directory Linux)
gravatar for biohacker_tobe
8 months ago by
biohacker_tobe40 wrote:


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
alignment msa sequence assembly • 246 views
ADD COMMENTlink modified 8 months ago by ATpoint41k • written 8 months ago by biohacker_tobe40
gravatar for Joe
8 months ago by
United Kingdom
Joe18k wrote:

This isn't how you do MSA, even with a small number of files. You need all the sequences to be in the same file, or you need to provide all the fasta's at once via STDIN (if the tool supports it).

cat *.faa > allseqs.fa
mafft allseqs.fa > output.msa
ADD COMMENTlink written 8 months ago by Joe18k

Thank you for the clarification, I am used to using mega or geneious for this. Best regards

ADD REPLYlink written 8 months ago by biohacker_tobe40
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