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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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Clarification regarding letterconf usage #81

Open microbearlogist opened 1 month ago

microbearlogist commented 1 month ago

Hi Robert,

Would it be possible to clarify a bit the expected input for the option letterconf?

muscle -letterconf ensemble.efa -ref aln.afa

What is the ensemble.efa? A diversified or a stratified ensemble or something else? If something else how to obtain it?

All the best, Ben

rcedgar commented 1 month ago

Any ensemble should work. I would tend to prefer diversified because it's more... diverse :-)

microbearlogist commented 1 month ago

Thanks a lot!

I thought I was providing a improper wrong input because I get an error when using the -html option

---Fatal error---
Bad conf=*

Seems that I found a bug (muscle 5.2.linux64)