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BAli-phy website  

BAli-phy is MCMC software developed by Ben Redelings with Marc Suchard for simultaneous Bayesian estimation of alignment and phylogeny (and other parameters). It handles generic Bayesian modeling via probabilistic programming.

BAli-Phy can estimate phylogenetic trees from sequence data when the alignment is uncertain. Instead of conditioning on a single alignment estimate, BAli-Phy accounts for alignment uncertainty by integrating over all alignments. BAli-Phy does not rely on a guide tree because the alignment and the tree are co-estimated. Therefore it can construct phylogeny estimates of widely divergent sequences without bias toward a guide tree.

Required Modules


  • gcc/5.2.0
  • bali-phy


module load gcc/5.2.0 bali-phy

System Variables

  • HPC_BALI-PHY_DIR - installation directory
  • HPC_BALI-PHY_BIN - executable program directory
  • HPC_BALI-PHY_LIB - library directory


- 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]