Introduction

09/09/14: BAli-Phy 2.3.5 released
Fix bugs, enable generic models (more news)

08/26/14: BAli-Phy used for large 117-taxon tree by McKenzie et. al.

05/27/14: Paper published: Erasing Errors Due to Alignment Ambiguity When Estimating Positive Selection (WWW)

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.

BAli-Phy also produces high-quality alignment estimates for highly divergent sequences, because it uses advanced substitution models and a realistic model of indels occurring on an (uncertain) tree. BAli-Phy can produce alignment uncertainty (AU) plots that are colored to indicate uncertain areas of the alignment.

BAli-Phy works on the nucleotide, amino acid, and codon levels and can utilize complex substitution models, such as GTR+gamma[n], WAG+log-normal[n]+INV, M0, M7, and more. It can be used to estimate substitution rates, frequencies, and indel rates when the tree and alignment are uncertain.

uncertain                                          certain
....310.......320.......330.......340.......350.......360.......370.......
Thermotoga DEVEIIGLSYEIKKTV---VTSVEMFRKELDEGIAGDNVGCLLRGIDKDEVERGQVLA-----APGSIKPHKRF
Anacystis ETIEIVGLR-DTRSTT---VTGVEMFQKTLDEGLAGDNVGLLLRGIQKTDIERGMVLA-----KPGSITPHTKF
Escheria EEVEIVGIK-ETQKST---CTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLA-----KPGTIKPHTKF
Pyrococcus EVVIFEPASTIFHKPIQGEVKSIEMHHEPLEEALPGDNIGFNVRGVSKNDIKRGDVAGHTTN-PPTVVRTKDTF
Halobacterium DNVSFQPSDVG------GEVKTIEMHHEEVPNAEPGDNVGFNVRGIGKDDIRRGDVCGPADD-PPSVA---DTF
Methanococcus DKVVFEPAGAI------GEIKTVEMHHEQLPSAEPGDNIGFNVRGVGKKDIKRGDVLGHTTN-PPTVA---TDF
Aeropyrum DKVVFMPPGVV------GEVRSIEMHYQQLQQAEPGDNIGFAVRGVSKSDIKRGDVAGHLDK-PPTVA---EEF
Sulfolobus DKIVFMPVGKI------GEVRSIETHHTKIDKAEPGDNIGFNVRGVEKKDVKRGDVAGSVQN-PPTVA---DEF
Giardia MKVVFAPTSQV------SEVKSVEMHHEELKKAGPGDNVGFNVRGLAVKDLKKGYVVGDVTNDPPVGC---KSF
Homo MVVTFAPVNVT------TEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEA---AGF
Euglena DVVTFAPNNLT------TEVKSVEMHHEALTEAVPGDNVGFNVKNVSVKDIRRGYVASNAKNDPAKEA---ADF
Nicotiana MVVTFGPTGLT------TEVKSVEMHHEALQEALPGDNVGFNVKNVAVKDLKRGFVASNSKDDPAKGA---ASF
 

References

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

comments and suggestions: benjamin . redelings * duke + edu