PhyloNet
PhyloNet (Phylogenetic Regulatory Network) is a tool package to analyze and reconstruct phylogenetic networks and evolutionary relationships from data sets of unlinked loci. The PhyloNet algorithms include Maximum Parsimony, likelihood, and Bayesian inference functions.
Topic
Sequences;Gene regulation;DNA
Detail
Operation: Motif discovery
Software interface: Command-line user interface
Language: Java
License: GNU Lesser General Public License v >=3
Cost: Free
Version name: 3.8.4
Credit: Department of Energy (DOE), National Institutes of Health (NIH), National Science Foundation (NSF), Sloan and Guggenheim fellowships, George R. Brown School of Engineering Roy E. Campbell Faculty Development Award, Department of Computer Science at Rice University.
Input: NEXUS, eNewick
Output: -
Contact: Luay Nakhleh nakhleh@rice.edu, Cuong Than cvthan@cs.rice.edu, Derek Ruths druths@cs.rice.edu
Collection: -
Maturity: Mature
Publications
- Inferring Phylogenetic Networks Using PhyloNet.
- Wen D, Yu Y, Zhu J, Nakhleh L (2018). Inferring Phylogenetic Networks Using PhyloNet. Syst Biol 67(4): 735-740.
- https://doi.org/10.1093/sysbio/syy015
- PMID: 29514307
- PMC: PMC6005058
- PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships.
- Than C, Ruths D, Nakhleh L (2008). PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinformatics 9: 322.
- https://doi.org/10.1186/1471-2105-9-322
- PMID: 18662388
- PMC: PMC2533029
Download and documentation
Source: https://github.com/NakhlehLab/PhyloNet/releases/tag/3.8.4
Documentation: https://wiki.rice.edu/confluence/pages/viewpage.action?pageId=39500205
Home page: https://bioinfocs.rice.edu/phylonet
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