Bug#891971: ITP: bali-phy -- Bayesian Inference of Alignment and Phylogeny
- Date: Sat, 03 Mar 2018 09:20:12 -0500
- From: Benjamin Redelings <benjamin.redelings@xxxxxxxxx>
- Subject: Bug#891971: ITP: bali-phy -- Bayesian Inference of Alignment and Phylogeny
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.