Bali-phy: simultaneous bayesian inference of alignment and phylogeny. Summary: BAli-Phy is a Bayesian posterior sampler that employs Markov chain Monte Carlo to explore the joint space of alignment and phylogeny given molecular sequence data. Simultaneous estimation eliminates bias toward inaccurate alignment guide-trees, employs more sophisticated substitution models during alignment and automatically utilizes information in shared insertion/deletions to help infer phylogenies. Availability: Software is available for download at http://www.biomath.ucla.edu/msuchard/bali-phy.
Keywords for this software
References in zbMATH (referenced in 6 articles )
Showing results 1 to 6 of 6.
- Bouchard-C^oté, Alexandre: A note on probabilistic models over strings: the linear algebra approach (2013)
- Daskalakis, Constantinos; Roch, Sebastien: Alignment-free phylogenetic reconstruction: Sample complexity via a branching process analysis (2013)
- Andoni, Alexandr; Daskalakis, Constantinos; Hassidim, Avinatan; Roch, Sebastien: Global alignment of molecular sequences via ancestral state reconstruction (2012)
- Wolfsheimer, Stefan; Hartmann, Alexander; Rabus, Ralf; Nuel, Gregory: Computing posterior probabilities for score-based alignments using ppALIGN (2012)
- Malaspinas, Anna-Sapfo; Eriksson, Nicholas; Huggins, Peter: Parametric analysis of alignment and phylogenetic uncertainty (2011)
- Luo, Ruiyan; Larget, Bret: Modeling substitution and indel processes for AFLP marker evolution and phylogenetic inference (2009)