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refresh-bio / FAMSA

Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)
GNU General Public License v3.0
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Question: how can we do profile alignment using FAMSA? #44

Closed PraljakReps closed 6 months ago

PraljakReps commented 1 year ago

I see that FAMSA allows for straightforward profile-profile alignment between MSAs using the following command: 

# profile-profile alignment without refining output 
./famsa -refine_mode off ./test/adeno_fiber/upgma.no_refine.part1.fasta ./test/adeno_fiber/upgma.no_refine.part2.fasta pp.fasta

It isn't clear to me based on the README.md on how to do profile alignment. I.e., how can I align a single sequence onto a desired MSA using FAMSA?