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rcedgar / muscle

Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.
https://drive5.com/muscle
GNU General Public License v3.0
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Stdin/stdout as input/output to muscle -align? #20

Closed amijalis closed 2 years ago

amijalis commented 2 years ago

This is more of a question than an issue, but can you use muscle-align using stdin and stdout?

Thanks!

rcedgar commented 2 years ago

Yes, for example:

cat input.fa | muscle -align /dev/stdin -output /dev/stdout | tee output.afa