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[BioStars] Removing gapped columns from a multiple sequence alignment
trimal -in test -out test_nogaps_trimal -nogaps
Uses a heuristic method to decide which is the best automated method to trim the input alignment.
trimal -in <inputfile> -out <outputfile> -automated1
FASconCAT PubMed https://www.zfmk.de/en/research/research-centres-and-groups/fasconcat