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¶

If you publish research that uses BALi-Phy you have to cite it as follows:

Redelings, B. D., & Suchard, M. A. (2005). Joint Bayesian estimation of alignment and phylogeny. Systematic Biology, 54(3), 401–418. https://doi.org/10.1080/10635150590947041
Suchard, M. A., & Redelings, B. D. (2006). BAli-Phy: Simultaneous Bayesian inference of alignment and phylogeny. Bioinformatics, 22(16), 2047–2048. https://doi.org/10.1093/bioinformatics/btl175
Redelings, B. D., & Suchard, M. A. (2007). Incorporating indel information into phylogeny estimation for rapidly emerging pathogens. BMC Evolutionary Biology, 7, 40. https://doi.org/10.1186/1471-2148-7-40
Redelings, B. D. (2014). Erasing errors due to alignment ambiguity when estimating positive selection. Molecular Biology and Evolution, 31(8), 1979–1993. https://doi.org/10.1093/molbev/msu173

Categories¶

phylogenetics