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
Westesson O, Barquist L, Holmes I "HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction." Bioinformatics. 2012 Apr 15;28(8):1170-1. https://doi.org/10.1093/bioinformatics/bts058
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 https://doi.org/10.1093/bioinformatics/btx558
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