BAli-Phy

News

9/12/26: BAli-Phy 4.3 is available for download (see changes).

Breaking changes
Many model and distribution names are now capitalized.
New features
Locate positive selection, even when the alignment is uncertain.
Visualize rates and dN/dS for individual letters or codons, including rate variation under heterotachy models.
A fuller range of codon analyses: single-ω analyses, site, branch, and branch-site tests.

Introduction

BAli-Phy is software by Ben Redelings and Marc Suchard 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.

High alignment accuracy: Redelings (2014) showed that BAli-Phy had 3.5 times fewer alignment errors than MUSCLEv4 and MAFFT on simulated data:

Figure 4. from Redelings BD. Erasing Errors Due to Alignment Ambiguity When Estimating Positive Selection. Mol. Biol. Evo. 31(8), 2014.

Eliminate bias: Fletcher and Yang (2010) showed that relying on a ClustalW alignment estimate could lead to a 99% false-positive rate in detecting positive selection. Evolutionary trees and branch lengths that are inferred from a single alignment can also be biased if the alignment is ambiguous. BAli-Phy solves the problem of alignment bias by using MCMC to estimate evolutionary trees, positive selection, and branch lengths while simultaneously averaging over alternative alignments in a Bayesian paradigm.

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
 

This ambiguity can be displayed graphically in an alignment uncertainty (AU) plot.

Model-based alignment: BAli-Phy can make use of complex substitution models while estimating alignments (and trees). These include the free-rates and Gamma+INV models, codon models such as the M3 and M8 models, and covarion models such as Tuffley-Steel.

Fixed-alignment: BAli-Phy can also estimate phylogenies from a fixed alignment (like MrBayes and BEAST) using complex substitution models like GTR+gamma.

Multi-gene: BAli-Phy automatically estimates relative rates for each gene, as described in the Manual and the tutorial.

Ancestral sequence reconstruction: BAli-Phy automatically reconstructs ancestral sequences (with gaps) for each gene, while averaging over both topological and alignment uncertainty, as described in the Manual.

References

  1. Redelings BD BAli-Phy version 3: model-based co-estimation of alignment and phylogeny.
    (2021) Bioinformatics 37(18). [doi:10.1093/bioinformatics/btab129]
  2. Redelings BD Erasing Errors Due to Alignment Ambiguity When Estimating Positive Selection.
    (2014) Mol. Biol. Evo. 31(8). [doi:10.1093/molbev/msu174]
  3. Redelings BD and Suchard MA Incorporating indel information into phylogeny estimation for rapidly emerging pathogens.
    (2007) BMC Evolutionary Biology, 7:40. [doi: 10.1186/1471-2148-7-40]
  4. Suchard MA and Redelings BD BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny.
    (2006) Bioinformatics, 22:2047-2048. [doi:10.1093/bioinformatics/btl175]
  5. Redelings BD and Suchard MA Joint Bayesian Estimation of Alignment and Phylogeny.
    (2005) Systematic Biology, 54(3):401-418 [doi:10.1080/10635150590947041]