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

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

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.

Network 4.613 – Phylogenetic Network Software

Network 4.613

:: 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

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.

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.

Quartet-net – Quartet-based method to Reconstruct Phylogenetic Networks

Quartet-net

:: DESCRIPTION

QuartetNet is a quartet based algorithm, as well as an implementing software suite, to reconstruct phylogenetic networks from weighted triplets and quartets.

::DEVELOPER

Systems Biology Laboratory, College of Veterinary Medicine,Mississippi State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

 QuartetNet

:: MORE INFORMATION

Citation

Mol Biol Evol. 2013 May;30(5):1206-17. doi: 10.1093/molbev/mst040.
Quartet-net: a quartet-based method to reconstruct phylogenetic networks.
Yang J, Grünewald S, Wan XF.

PhyloNetwork – Alignment of Phylogenetic Networks

PhyloNetwork

:: DESCRIPTION

PhyloNetwork relies on the BioPerl bundle and implements several algorithms on phylogenetic networks, from parsing and temporal representation to distances between phylogenetic networks and optimal alignments.

::DEVELOPER

Biel Cardona , F. Rosselló, Gabriel Valiente

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Perl

:: DOWNLOAD

 PhyloNetwork

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2008 Mar 27;9:175. doi: 10.1186/1471-2105-9-175.
A perl package and an alignment tool for phylogenetic networks.
Cardona G, Rosselló F, Valiente G.