News

7/16/22: BAli-Phy 4.0-alpha6 is available for download on github.
BAli-Phy 4.0 will likely be released around Jan 2023.

08/24/21: BAli-Phy 3.6.1 released - Download
Bug fixes for BES (See release notes)

03/02/21: Paper - BAli-Phy version 3: Model-based co-estimation of Alignment and Phylogeny

Introduction

BAli-Phy is software by Ben Redelings 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. It has been used in published analyses on data sets up to 117 taxa.

High alignment accuracy: Redelings (2014) showed that BAli-Phy had 3.5 times fewer alignment errors than MUSCLE 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]

comments and suggestions: benjamin . redelings * gmail + com