HmmCleaner is a tool to remove alignment and sequencing error containing segments from multiple sequence alignments (MSA) using profile hidden Markov models (pHMM). This tool is based on Bio::MUST modules and integrates into MUST environment.
Phylogeny; Sequence analysis; Nucleic acid sites, features and motifs; Nucleic acid structure analysis; Sequence sites, features and motifs
Di Franco A, Poujol R, Baurain D, Philippe H "Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences." BMC Evol Biol. 2019 Jan 11;19(1):21. https://doi.org/10.1186/s12862-019-1350-2
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