SplitsTree 6.1.10 – Compute Phylogenetic Networks

SplitsTree 6.1.10

:: DESCRIPTION

SplitsTree uses the split decomposition method to analyse and visualize distance data, e.g. data derived from biosequences. SplitsTree4 is the leading application for computing unrooted phylogenetic networks from molecular sequence data. Given an alignment of sequences, a distance matrix or a set of trees, the program will compute a phylogenetic tree or network using methods such as split decomposition, neighbor-net, consensus network, super networks methods or methods for computing hybridization or simple recombination networks.

::DEVELOPER

the Algorithms in Bioinformatics lab.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX

:: DOWNLOAD

SplitsTree

:: MORE INFORMATION

Citation

D. H. Huson and D. Bryant,
Application of Phylogenetic Networks in Evolutionary Studies
Mol. Biol. Evol., 23(2):254-267, 2006.

Network 10.2.0.0 – Phylogenetic Network Software

Network 10.2.0.0

:: 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

Fluxus Technology Ltd

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Network

:: MORE INFORMATION

PhyloNetworks v0.14.2 – Analysis for Phylogenetic Networks

PhyloNetworks v0.14.2

:: DESCRIPTION

PhyloNetworks is a Julia package for the inference, manipulation, visualization, and use of phylogenetic networks in an interactive environment.

::DEVELOPER

Solis-Lemus lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOs
  • Julia

:: DOWNLOAD

PhyloNetworks

:: 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.

MC-NET 1.0 – Construction of Phylogenetic Networks

MC-NET 1.0

:: DESCRIPTION

MC-Net is A method for the construction of phylogenetic networks based on Monte-Carlo method

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • MatLab

:: DOWNLOAD

 MC-NET

:: MORE INFORMATION

Citation

BMC Evol Biol. 2010 Aug 20;10:254. doi: 10.1186/1471-2148-10-254.
MC-Net: a method for the construction of phylogenetic networks based on the Monte-Carlo method.
Eslahchi C1, Habibi M, Hassanzadeh R, Mottaghi E.

TCS 1.21 – Phylogenetic Network Estimation using Statistical Parsimony

TCS 1.21

:: DESCRIPTION

TCS is a Java computer program to estimate gene genealogies including multifurcations and/or reticulations (i.e. networks). The network estimation implemented in TCS is also known as Statistical Parsimony. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132:619-633.

::DEVELOPER

Computational Science Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

TCS

:: MORE INFORMATION

Citation

Clement M, Posada D and Crandall K. 2000.
TCS: a computer program to estimate gene genealogies.
Molecular Ecology 9(10): 1657-1660

NetworkDiversity 1.0.0 – Calculation of beta diversity over Phylogenetic Networks

NetworkDiversity 1.0.0

:: DESCRIPTION

Network Diversity  is a software package for calculating beta diversity over split systems, a widely used class of implicit phylogenetic networks.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows /MacOsX
  • C++ Compiler

:: DOWNLOAD

 Network Diversity

:: MORE INFORMATION

Citation

Mol Biol Evol. 2012 Dec;29(12):3947-58. doi: 10.1093/molbev/mss200.
Measuring community similarity with phylogenetic networks.
Parks DH, Beiko RG.

MCQ-Net – Constructing Phylogenetic Networks from Weighted Quartets

MCQ-Net

:: DESCRIPTION

MCQ-Net is a heuristic algorithm based on the simulated annealing as a method for constructing phylogenetic networks from weighted quartets.

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • MatLab

:: DOWNLOAD

 MCQ-Net

:: MORE INFORMATION

MY-CLOSURE 1.0 – Computing a Phylogenetic Network from a collection of Phylogenetic Trees

MY-CLOSURE 1.0

:: DESCRIPTION

MY-CLOSURE is a Java program for computing a phylogenetic network from a collection of phylogenetic trees.

::DEVELOPER

The UEA Computational Biology Laboratory at the University of East Anglia (UEA)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java

:: DOWNLOAD

 MY-CLOSURE

:: MORE INFORMATION

Citation

S. Grunewald, K. T. Huber and Q. Wu,
2 Novel Closure Rules for Constructing Phylogenetic Super-networks,
Bulletin of Mathematical Biology, 70: 1906-1924, 2008

TriLoNet 1.0 – Construct Rooted Level-1 Phylogenetic Networks

TriLoNet 1.0

:: DESCRIPTION

TriLoNet is a Java software package created to construct rooted level-1 phylogenetic networks from aligned DNA sequence data. The software package consists of two modules:

TriLoNet – constructs level-1 phylogenetic networks from a dense collection of trinets
SeqTrinet – constructs a dense set of trinets from a multiple sequence alignment

::DEVELOPER

The UEA Computational Biology Laboratory at the University of East Anglia (UEA)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

 TriLoNet

:: MORE INFORMATION

Citation

TriLoNet: Piecing Together Small Networks to Reconstruct Reticulate Evolutionary Histories.
Oldman J, Wu T, van Iersel L, Moulton V.
Mol Biol Evol. 2016 Apr 15. pii: msw068.

TripNet – Constructing Phylogenetic Networks from Sparse Sets of Rooted Triplets

TripNet

:: DESCRIPTION

TripNet is an algorithm for constructing phylogenetic networks from sparse sets of rooted triplets.

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • MatLab

:: DOWNLOAD

 TripNet

:: MORE INFORMATION

Citation

PLoS One. 2014 Sep 10;9(9):e106531. doi: 10.1371/journal.pone.0106531. eCollection 2014.
TripNet: a method for constructing rooted phylogenetic networks from rooted triplets.
Poormohammadi H, Eslahchi C, Tusserkani R

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