BAli---Phy

Bayesian Alignment and Phylogeny estimation

Introduction

04/08/14: Submitted revised manuscript:
Erasing Errors Due to Alignment Ambiguity When Estimating Positive Selection (PDF)

12/30/13: BAli-Phy 2.2.0 released
Successfully accounts for alignment uncertainty in testing for (diversifying) positive selection. (What else is new?)

06/23/12: Branch-site model for positive selection - presented at SMBE2012

05/01/11: Success with large 68-taxon tree!
See Gaya et al (2011) for information on models and convergence criteria.

02/03/11: BAli-Phy 2.1.1 released
This release fixes a few bugs. (What else is new?)

BAli-Phy is MCMC software developed by Ben Redelings with Marc Suchard for simultaneous Bayesian estimation of alignment and phylogeny (and other parameters). [See the paper and the Application Note.]

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]

[See more papers on statistical alignment on my "links" page.]


comments and suggestions: benjamin . redelings * duke + edu