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HandAlign is a part of the DART package and a tool for reconstruction of multiple sequence alignment (MSA) and phylogenetic history. HandAlign includes several Metropolis-Hastings Markov chain Monte Carlo (MCMC) for sampling of any target distribution.


RNA-seq; Mapping; Transcription factors and regulatory sites


  • Operation: Multiple sequence alignment
  • Input: FASTA, Stockholm, Stockholm Newick
  • Output: Stockholm Newick
  • Software interface: Command-line user interface
  • Language: C++
  • Operating system: Linux
  • License: GNU GPL v2
  • Cost: Free
  • Version name: -
  • Maturity: Stable
  • Credit: National Institutes of Health/National Human Genome Research Institute grant (R01-GM076705).
  • Contact: Ian Holmes ihh _at_
  • Collection: DART


Westesson O, Barquist L, Holmes I "HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction." Bioinformatics. 2012 Apr 15;28(8):1170-1.
PMID: 22285828
PMCID: PMC3324510

Lin HN, Hsu WL "DART - a fast and accurate RNA-seq mapper with a partitioning strategy." Bioinformatics, Volume 34, Issue 2, 15 January 2018, Pages 190–197
PMID: 28968831
PMCID: PMC5860201

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