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PhyloNetwork specifications

Information


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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Maintainer


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Information


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

Maintainer


This tool is not available anymore.

Publications for PhyloNetwork

PhyloNetwork in pipeline

2012
PMCID: 3458055
PMID: 23049811
DOI: 10.1371/journal.pone.0045527

[…] using the majority rule in the consense program., this binary matrix was also used to reconstruct a median joining network, using networks 4.5 (http://www.fluxus-engineering.com/), and a neighbornet phylonetwork, using splitstree 4 package ., phylogenetic relationships between s. cerevisiae x s. kudriavzevii natural hybrids obtained from several origins and a set of pure strains of the two […]


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PhyloNetwork in publications

 (4)
PMCID: 5784728
PMID: 29416568
DOI: 10.1186/s13100-018-0111-x

[…] evolutionary relationships among dnabi from cpdna and bacteria, we utilized an alignment-based approach for phylogenetic network inference (fig. ; additional file ) []. as evident from the resulting phylonetwork (fig. ; additional file : figure s6), some bacterial and cpdna dnabi are distantly related as they cluster together on the same branches, suggesting intein transfer by endosymbiosis., […]

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

[…] publication costs were funded by the singapore ministry of education academic research fund moe2014-t2-1-155., the programs and related data are available for download on https://github.com/icelu/phylonetwork., project design: lxz. program implementation and experiments: bxl. manuscript preparation: bxl, lxz and hwl. all authors read and approved the final manuscript., the authors declare […]

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

[…] 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, […]

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

[…] 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., we used nettest to analyze a large group of nucleotide […]


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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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