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PhyloNetwork specifications


Unique identifier OMICS_10319
Name PhyloNetwork
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability No
Maintained No




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Unique identifier OMICS_10319
Name PhyloNetwork
Interface Web user interface
Restrictions to use None
Programming languages Perl
Computer skills Basic
Stability No
Maintained No


This tool is not available anymore.

Publications for PhyloNetwork

PhyloNetwork citations


The dynamic intein landscape of eukaryotes

PMCID: 5784728
PMID: 29416568
DOI: 10.1186/s13100-018-0111-x

[…] -based approach (Fig. ), which is less constrained and represents simultaneous interrelationships of all sequences based on their pairwise alignments [].Based on the results of our SSN and additional phylonetwork analyses (Fig. ), we propose a model for intein dissemination in eukaryotes involving vertical inheritance, intragenomic mobility, endosymbiotic and horizontal (extragenomic) acquisitions […]


A program to compute the soft Robinson–Foulds distance between phylogenetic networks

BMC Genomics
PMCID: 5374702
PMID: 28361712
DOI: 10.1186/s12864-017-3500-5

[…] The programs and related data are available for download on […]


Complex Ancestries of Lager Brewing Hybrids Were Shaped by Standing Variation in the Wild Yeast Saccharomyces eubayanus

PLoS Genet
PMCID: 4934787
PMID: 27385107
DOI: 10.1371/journal.pgen.1006155

[…] olina and Tibet), the value of the log2 of the ratio of the d values were calculated for each window (see ).The whole genome phylogenetic tree was reconstructed from WGS data using RAxML v8.1 []. For phylonetwork and population analyses, SNPs were selected using strict coverage and quality filters (details in ). Based on the comparisons of the log2 divergence ratios or the PCAdmix results, genomic […]


Reconstruction of the Evolutionary History of Saccharomyces cerevisiae x S. kudriavzevii Hybrids Based on Multilocus Sequence Analysis

PLoS One
PMCID: 3458055
PMID: 23049811
DOI: 10.1371/journal.pone.0045527

[…] by using the majority rule in the Consense program.This binary matrix was also used to reconstruct a Median Joining Network, using Networks 4.5 (, and a NeighborNet Phylonetwork, using SPLITSTREE 4 package . […]


Characterization of phylogenetic networks with NetTest

BMC Bioinformatics
PMCID: 2880032
PMID: 20487540
DOI: 10.1186/1471-2105-11-268

[…] load or paste the network in different formats (see Results). The analysis pipeline was developed in Perl using CGI (Common Gateway Interface). The network classification uses the BioPerl module Bio::PhyloNetwork []. The web server uses the Apache HTTP server and was tested and verified using Firefox, Safari, and Internet Explorer. […]


Extended Newick: it is time for a standard representation of phylogenetic networks

BMC Bioinformatics
PMCID: 2621367
PMID: 19077301
DOI: 10.1186/1471-2105-9-532

[…] several Newick strings as the representation of a single phylogenetic network, and the first proposal was adopted with a few minor improvements. The agreed-upon standard was then included in the Bio::PhyloNetwork package for phylogenetic networks in Perl [] and made available as part of the BioPerl bundle []. The extended Newick format is described in detail in the Results section.Later on, howeve […]


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PhyloNetwork institution(s)
Department of Mathematics and Computer Science, University of the Balearic Islands, Palma de Mallorca, Spain; Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, Barcelona, Spain

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