FAMSA is designed to produce rapid multiple sequence alignment of large protein families. It first determines the longest common subsequences and has a unique way to compute gap costs. It proceeds progressively to add sequences into the alignments using a novel iterative approach. The Authors claim FAMSA to be superior to Clustal Omega and MAFFT. A GPU version is available.
Phylogeny; Sequence analysis; Nucleic acid sites, features and motifs; Nucleic acid structure analysis; Sequence sites, features and motifs
Deorowicz S, Debudaj-Grabysz A, Gudys A "FAMSA: Fast and accurate multiple sequence alignment of huge protein families." Sci Rep. 2016 Sep 27;6:33964. https://doi.org/10.1038/srep33964
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