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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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@ in output filename required for -perm all with -super5 #62

Closed DeadlineWasYesterday closed 5 days ago

DeadlineWasYesterday commented 1 year ago

According to the documentation, it should just make one ensemble .efa file with all four guide trees if I don't include the '@' wildcard. But my muscle 5.1 errors out forcing me to use an @ to write 4 separate files which I then have to join with -fa2efa. Is this intended?

rcedgar commented 1 year ago

This is a documentation problem, I will add the following text to the usage help in the next build:

Note -super5 does not support .efa output, to get an ensemble you can
  (1) run several times with different -perm and -perturb options, or
  (2) use -perm all, then four output files will be generated, one for
        each guide tree permutation (use @ in the output filename).