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BAli-Phy specifications


Unique identifier OMICS_03734
Name BAli-Phy
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some molecular sequences and alignments.
Input format FASTA,PHYLIP
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes




No version available



  • person_outline Marc Suchard

Publications for BAli-Phy

BAli-Phy citations


Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution

BMC Genomics
PMCID: 5941490
PMID: 29739321
DOI: 10.1186/s12864-018-4711-0

[…] We also examined whether alignment error affected branch tests. For single-copy gene families that had a significant branch test from PAML, we ran BAli-Phy for one chain of 10,000 iterations under a codon model with a single dN/dS across all branches and randomly sampled 100 alignments without burn-in, as the MCMC chain started with the MUSCLE a […]


Sharing of photobionts in sympatric populations of Thamnolia and Cetraria lichens: evidence from high throughput sequencing

Sci Rep
PMCID: 5849601
PMID: 29535321
DOI: 10.1038/s41598-018-22470-y

[…] sequences (ITS1 region) amplified with Sanger and Ion Torrent and the GenBank references (Table ) presented many ambiguously aligned regions. To be able to use all sequence information, the software BAli-Phy 2.3.8, which simultaneously estimates the alignment and the phylogeny using Bayesian inference, was used. We used JModel test to define HKY with a gamma distribution as the nucleotide substit […]


Cultivation and Genomic Analysis of “Candidatus Nitrosocaldus islandicus,” an Obligately Thermophilic, Ammonia Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland

Front Microbiol
PMCID: 5817080
PMID: 29491853
DOI: 10.3389/fmicb.2018.00193

[…] ngs in mafft () and a phylogenetic tree was calculated using FastTree ().Nitrilase superfamily amino acid sequences were obtained from . Alignment and phylogenetic reconstruction was carried out with Bali-Phy (; randomize alignment, iterations = 11000, burnin = 6000). Posterior tree pools from 10 independent runs were combined to generate a 50% PP consensus tree and to assess bipartition support.A […]


Pherotype Polymorphism in Streptococcus pneumoniae Has No Obvious Effects on Population Structure and Recombination

Genome Biol Evol
PMCID: 5629823
PMID: 28992304
DOI: 10.1093/gbe/evx188
call_split See protocol

[…] tis (45 genomes), S. oralis (18 genomes), and S. pseudopneumoniae (40 genomes). The extensive sequence diversity in the mature CSP meant that we lacked confidence in aligning comC. Therefore, we used BAli-Phy v.2.3.6 () for phylogenetic analysis because it estimates both the alignment and the tree simultaneously. We used the HKY+ γ model of substitution and constrained the leader sequence of comC […]


Increased Affinity for RNA Targets Evolved Early in Animal and Plant Dicer Lineages through Different Structural Mechanisms

Mol Biol Evol
PMCID: 5850739
PMID: 29106606
DOI: 10.1093/molbev/msx187

[…] ed the psicoffee alignment mode, with ancestral sequences reconstructed directly from this alignment, assuming the consensus phylogeny. Finally, we reconstructed alternative ancestral sequences using BAli-Phy v3.0 beta1, which uses a Bayesian approach to sample sequence alignments and trees from the combined posterior probability distribution (; ). BAli-Phy analysis was run using the LG + F substi […]


A Generative Angular Model of Protein Structure Evolution

Mol Biol Evol
PMCID: 5850488
PMID: 28453724
DOI: 10.1093/molbev/msx137

[…] heless, a single Maximum A Posteriori (MAP) pairwise alignment may be obtained from the alignment samples and used for downstream analysis.ETDBN and several other alignment methods (namely StatAlign, BAli-Phy, MUSCLE, and MAFFT) were used to infer pairwise alignments from simulated and real data under various combinations of data observations, for example: an amino acid sequence pair (Aa, Ab), a s […]


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BAli-Phy institution(s)
Biology Department, Duke University, Durham, NC, USA; The National Evolutionary Synthesis Center, Durham, NC, USA
BAli-Phy funding source(s)
Supported by National Science Foundation Grant #EF-0905606 to the National Evolutionary Synthesis Center (NESCent) and by Public Health Service grant #GM-37841.

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