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Bug#891971: ITP: bali-phy -- Bayesian Inference of Alignment and Phylogeny




Package: wnpp
Severity: wishlist
Owner: Benjamin Redelings <benjamin.redelings@xxxxxxxxx>

* Package name    : bali-phy
  Version         : 3.0
  Upstream Author : Benjamin Redelings <benjamin.redelings@xxxxxxxxx>
* URL             : http://www.bali-phy.org/
* License         : (GPL)
  Programming Lang: (C++)
  Description     : Bayesian Inference of Alignment and Phylogeny

 BAli-Phy estimates multiple sequence alignments and evolutionary trees
 from unaligned DNA, amino acid, or codon sequences.  BAli-Phy uses MCMC
 to estimate evolutionary trees, positive selection, and branch lengths
 while averaging over alternative alignments. BAli-Phy can display
 alignment ambiguity graphically in an alignment uncertainty (AU) plot.
 .
 BAli-Phy can also estimate phylogenies from a fixed alignment (like MrBayes
 and BEAST) using substitution models like GTR+gamma.  BAli-Phy automatically
 estimates relative rates for each gene.

- Why is this package relevant?

This package performs Bayesian inference of alignment, as well as inference of phylogeny like mrbayes, beast-mcmc, beast2-mcmc, etc.  This package produces higher quality alignments than programs like fsa, mafft, muscle, at the cost of taking much longer to run.

- How do you plan to maintain it?

I hope to maintain it myself.  I am looking for a mentor.