:: DESCRIPTION
Network is used to reconstruct phylogenetic networks and trees, infer ancestral types and potential types, evolutionary branchings and variants, and to estimate datings. Network generates evolutionary trees and networks from genetic, linguistic, and other data. Network can then provide age estimates for any ancestor in the tree.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
NimbleTree is a relatively user-friendly Windows program for making phylogenetic trees starting from sequence data.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Before you download software you need to read disclaimer.
:: DESCRIPTION
ProtASR is an evolutionary framework to reconstruct ancestral protein sequences accounting for structural constraints.
::DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Arenas M, Weber CC, Liberles DA, Bastolla U.
ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability.
Syst Biol. 2017 Nov 1;66(6):1054-1064. doi: 10.1093/sysbio/syw121. PMID: 28057858.
:: DESCRIPTION
iBPP is a program of integration of genes and traits for Bayesian Phylogenetics and Phylogeography.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Solís-Lemus C, Knowles LL, Ané C.
Bayesian species delimitation combining multiple genes and traits in a unified framework.
Evolution. 2015 Feb;69(2):492-507. doi: 10.1111/evo.12582. Epub 2015 Jan 16. PMID: 25495061.
:: DESCRIPTION
PhyloNetworks is a Julia package for the inference, manipulation, visualization, and use of phylogenetic networks in an interactive environment.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Solís-Lemus C, Bastide P, Ané C.
PhyloNetworks: A Package for Phylogenetic Networks.
Mol Biol Evol. 2017 Dec 1;34(12):3292-3298. doi: 10.1093/molbev/msx235. PMID: 28961984.
:: DESCRIPTION
GO4genome is a prokaryotic phylogeny based on genome organization.
::DEVELOPER
Computational Protein Design and Evolution at the University of Regensburg
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Mol Evol. 2009 May;68(5):550-62. doi: 10.1007/s00239-009-9233-6.
GO4genome: a prokaryotic phylogeny based on genome organization.
Merkl R, Wiezer A.
:: DESCRIPTION
Crimson facilitates the extraction of sub-trees from very large phylogenetic trees.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Phylo-SMC is a Bayesian phylogenetic inference tool based on Sequential Monte Carlo (SMC), an alternative to the standard Markov Chain Monte Carlo approach (MCMC).
::DEVELOPER
Alexandre Bouchard, Sriram Sankararaman, and Michael I. Jordan
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Syst Biol. 2012 Jul;61(4):579-93. doi: 10.1093/sysbio/syr131.
Phylogenetic inference via sequential Monte Carlo.
Bouchard, A., Sankararaman, S., Jordan, M.I
:: DESCRIPTION
TAGD will generate tags for a specific branch of a tree, given the tree’s structure as well as the sequence for all its taxa.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
S. Angelov, B. Harb, S. Kannan, S. Khanna, and J. Kim. 2007.
“Efficient Enumeration of Phylogenetically Informative Substrings.”
Journal of Computational Biology., 14(6): 701-723.
:: DESCRIPTION
LGTNet is a software to infer networks of lateral genetic transfer (LGT) from sequence data. In contrast to traditional techniques based on multiple sequence alignments and phylogenetic trees LGTNet is an alignment- and tree-free method.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
S. Maetschke, L. McIntyre, C. Chan, M. Ragan
Fast inference of lateral genetic transfer networks.
