BAli---Phy

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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:

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.

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.