HmmCleaner

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.

Topic

Phylogeny;Sequence analysis;Nucleic acid sites, features and motifs;Nucleic acid structure analysis;Sequence sites, features and motifs

Detail

  • Operation: Multiple sequence alignment;Filtering

  • Software interface: Command-line user interface

  • Language: Perl

  • License: GNU GPL v1+

  • Cost: Free

  • Version name: 0.180750

  • Credit: Canadian Research Chair program and Natural Sciences and Engineering Research Council;The TULIP Laboratory of Excellence (ANR-10-LABX-41).

  • Input: List of alignment files

  • Output: MUST

  • Contact: herve.philippe@sete.cnrs.fr | rnaud.difranco@gmail.fr

  • Collection: -

  • Maturity: Stable

Publications

  • Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences.
  • Di Franco A, et al. Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences. Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences. 2019; 19:21. doi: 10.1186/s12862-019-1350-2
  • https://doi.org/10.1186/s12862-019-1350-2
  • PMID: 30634908
  • PMC: PMC6330419

Download and documentation

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