Multiple Sequence Alignment (Same Directory Linux)
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Entering edit mode
13 months ago

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 :)

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

msa assembly sequence alignment • 382 views
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Entering edit mode
13 months ago
Joe 19k

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

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Entering edit mode

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