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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


  • Operation: Multiple sequence alignment; Filtering
  • Input: List of alignment files
  • Output: MUST
  • Software interface: Command-line user interface
  • Language: Perl
  • Operating system: Linux; MAC OS X; Microsoft Windows
  • License: GNU GPL v1+
  • Cost: Free
  • Version name: 0.180750
  • Maturity: Stable
  • Credit: Canadian Research Chair program and Natural Sciences and Engineering Research Council;The TULIP Laboratory of Excellence (ANR-10-LABX-41).
  • Contact: herve.philippe _at_ | rnaud.difranco _at_
  • Collection: -


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.
PMID: 30634908
PMCID: PMC6330419

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