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

Network 5.011 – Phylogenetic Network Software

Network 5.011

:: 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

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.

SplitsTree 5.0.20 – Compute Phylogenetic Networks

SplitsTree 5.0.20

:: 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.

BIMLR 20130421 – Constructing Phylogenetic Networks from Phylogenetic trees

BIMLR 20130421

:: DESCRIPTION

BIMLR is a method for constructing rooted phylogenetic networks from rooted phylogenetic trees.

::DEVELOPER

NClab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 BIMLR

:: MORE INFORMATION

Citation

Gene. 2013 Sep 15;527(1):344-51. doi: 10.1016/j.gene.2013.06.036. Epub 2013 Jun 28.
BIMLR: a method for constructing rooted phylogenetic networks from rooted phylogenetic trees.
Wang J1, Guo M, Xing L, Che K, Liu X, Wang C.

LNETWORK 20140320 – An Efficient and Effective Method for Constructing Phylogenetic Networks

LNETWORK 20140320

:: DESCRIPTION

LNETWORK is an efficient and effective method for constructing phylogenetic networks.LNetwork takes as input a set of rooted phylogenetic trees given in Newick format (inputfile shows an example of input data).

::DEVELOPER

NClab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 LNETWORK

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Sep 15;29(18):2269-76. doi: 10.1093/bioinformatics/btt378. Epub 2013 Jun 29.
LNETWORK: an efficient and effective method for constructing phylogenetic networks.
Wang J1, Guo M, Liu X, Liu Y, Wang C, Xing L, Che K.

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.

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