Package: wnpp Severity: wishlist Owner: Benjamin Redelings <benjamin.redeli...@gmail.com>
* Package name : bali-phy Version : 3.0 Upstream Author : Benjamin Redelings <benjamin.redeli...@gmail.com> * 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.
