Closed DeadlineWasYesterday closed 5 days 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).
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?