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PhyloNet specifications


Unique identifier OMICS_06050
Name PhyloNet
Alternative name Phylogenetic Networks Toolkit
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Advanced
Version 3.6.8
Stability Stable
Maintained Yes






No version available


  • person_outline Luay Nakhleh
  • person_outline David Bryant
  • person_outline Yaxuan Wang

Additional information

Publications for Phylogenetic Networks Toolkit

PhyloNet citations


Structure and phylogeography of two tropical predators, spinner (Stenella longirostris) and pantropical spotted (S. attenuata) dolphins, from SNP data

R Soc Open Sci
PMCID: 5936904
PMID: 29765639
DOI: 10.1098/rsos.171615
call_split See protocol

[…] Phylogeographic analyses were performed using SNAPP, a Markov chain Monte Carlo (MCMC) sampler for bi-allelic data used to infer phylogenetic trees []. Because of the high number of SNP loci for each individual and because phylogenetic analyses o […]


Whole genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow

Sci Adv
PMCID: 5884691
PMID: 29632892
DOI: 10.1126/sciadv.aap9873

[…] on signals that are independent of the evolutionary placement of gray whales.In addition to character-based parsimony analysis, gene flow may preferably be studied by topology-based ML analysis using PhyloNet (). PhyloNet identifies a statistically significant signal for gene flow between the minke whale and the ancestor of the other rorquals (). With equal likelihood probability, gene flow occurr […]


Genomic evidence of speciation reversal in ravens

Nat Commun
PMCID: 5834606
PMID: 29500409
DOI: 10.1038/s41467-018-03294-w

[…] bour-Net analyses in SplitsTree v4.14.2 used uncorrected P distances and average states for heterozygous sites. Species trees were estimated in BEAST v2.4.3 using *BEAST for the autosomal introns and SNAPP for the SNP data sets. *BEAST species tree analyses on the autosomal intron data set used a Yule speciation prior and applied a lognormal prior on birthrate (M = 4.0, S = 1.25) and population me […]


Hidden endemism, deep polyphyly, and repeated dispersal across the Isthmus of Tehuantepec: Diversification of the White‐collared Seedeater complex (Thraupidae: Sporophila torqueola)

Ecol Evol
PMCID: 5792519
PMID: 29435260
DOI: 10.1002/ece3.3799
call_split See protocol

[…] nerated a panel of 12510 loci and 44 individuals for the S. t. morelleti cluster and 12,912 loci and 19 individuals for the S. t. torqueola cluster.We built species trees from biallelic SNPs with the SNAPP module (Bryant, Bouckaert, Felsenstein, Rosenberg, & RoyChoudhury, ) run with the program BEAST v2 (Bouckaert et al., ) to examine empirical support for different species delimitation scenarios […]


Gene flow analysis method, the D statistic, is robust in a wide parameter space

BMC Bioinformatics
PMCID: 5759368
PMID: 29310567
DOI: 10.1186/s12859-017-2002-4

[…] thods can be generally separated into two categories: likelihood-based/Bayesian- and parsimony-based, using different interpretations of the coalescent models. Likelihood or Bayesian methods, such as Phylonet [, ] and CoalHMM [] are based on a priori evolutionary models, and are applicable across a large range of conditions. However, their disadvantages often include excessive computation times an […]


Domestication Genomics of the Open Pollinated Scarlet Runner Bean (Phaseolus coccineus L.)

Front Plant Sci
PMCID: 5694824
PMID: 29187858
DOI: 10.3389/fpls.2017.01891
call_split See protocol

[…] ree () software. Lastly, we employed a Bayesian multispecies coalescent model () to estimate the phylogenetic relationships among well-supported clades within P. coccineus solely. We used the program SNAPP 1.3.0 (), included in the package BEAST 2.4.5 () to infer species trees directly from biallelic genetic data. We used the eight main genetic clusters (see section Results) inferred by Admixture […]


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PhyloNet institution(s)
Department of Computer Science, Rice University, Houston, TX, USA; Department of BioSciences, Rice University, Houston, TX, USA
PhyloNet funding source(s)
Supported by grants DBI-1355998, CCF-1302179, CCF-1514177 and DMS-1547433 from the National Science Foundation.

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