BALi-Phy¶

Description¶

BAli-Phy is software by Ben Redelings that estimates multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences. It uses likelihood-based evolutionary models of substitutions and insertions and deletions to place gaps. It has been used in published analyses on data sets up to 117 taxa.

Environment Modules¶

Run module spider bali-phy to find out what environment modules are available for this application.

Environment Variables¶

HPC_BALIPHY_DIR - installation directory
HPC_BALIPHY_BIN - executable directory
HPC_BALIPHY_LIB - library directory

Citation¶

Redelings BD and Suchard MA Joint Bayesian Estimation of Alignment and Phylogeny, Systematic Biology, 54(3):401-418, 2005 [PDF]
Suchard MA and Redelings BD BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny, Bioinformatics, 22:2047-2048, 2006. [PDF]
Redelings BD and Suchard MA. Incorporating indel information into phylogeny estimation for rapidly emerging pathogens. BMC Evolutionary Biology, 7:40, 2007. [PDF]
Redelings BD. Erasing Errors Due to Alignment Ambiguity When Estimating Positive Selection. Mol. Biol. Evo. 31(8), 2014. [WWW]

Categories¶

phylogenetics