Category: Phylogenetic Analysis

MEGA 12.1 – Molecular Evolutionary Genetics Analysis

MEGA 12.1

:: DESCRIPTION

MEGA （Molecular Evolutionary Genetics Analysis）is an integrated tool for automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.

::DEVELOPER

MEGA Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX

:: DOWNLOAD

MEGA

:: MORE INFORMATION

Citation

Mol Biol Evol. 2013 Dec;30(12):2725-9. doi: 10.1093/molbev/mst197. Epub 2013 Oct 16.
MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S.

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S (2011)
MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods.
Molecular Biology and Evolution (2011)doi: 10.1093/molbev/msr121 First published online: May 4, 2011

DARwin 6.0.021 – Diversity and Phylogenetic Analysis

DARwin 6.0.021

:: DESCRIPTION

DARwin (Dissimilarity Analysis and Representation for Windows) is a software package developed for diversity and phylogenetic analysis on the basis of evolutionary dissimilarities.

::DEVELOPER

DARwin Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 DARwin

:: MORE INFORMATION

Citation:

Perrier, X., Flori, A. , Bonnot, F. (2003). Data analysis methods.
In: Hamon, P., Seguin, M., Perrier, X. ,Glaszmann, J. C. Ed., Genetic diversity of cultivated tropical plants. Enfield, Science Publishers. Montpellier. pp 43 – 76.

HyperTree 1.2.2 – Java Phylogenetic Tree Viewer

HyperTree 1.2.2

:: DESCRIPTION

HYPERTREE is a Java phylogenetic tree viewer, with a hyperbolic (‘fish-eye’) view and editing abilities that help in managing very large trees.

::DEVELOPER

kinase.com

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

 HyperTree

:: MORE INFORMATION

Citation

Visualizing harge hierarchical clusters in hyperbolic space
J. Bingham, S Sudarsanam
Bioinformatics (2000) 16(7): 660-1

PhyloBayes 4.1c – Bayesian Phylogenetic software based on Mixture Models

PhyloBayes 4.1c

:: DESCRIPTION

PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments. Compared to other phylogenetic MCMC samplers (e.g. MrBayes), the main distinguishing feature of PhyloBayes is the underlying probabilistic model, CAT. It is particularly well suited for large multigene alignments, such as those used in phylogenomics.

::DEVELOPER

Nicolas Lartillot (nicolas.lartillot@umontreal.ca)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

 PhyloBayes

:: MORE INFORMATION

Citation

Nicolas Lartillot, Thomas Lepage and Samuel Blanquart
PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating
Bioinformatics (2009) 25 (17): 2286-2288.

FigTree 1.4.4 – Produce Figures of Phylogenetic Trees

FigTree 1.4.4

:: DESCRIPTION

FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. In particular it is designed to display summarized and annotated trees produced by BEAST.

::DEVELOPER

Andrew Rambaut Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java

:: DOWNLOAD

FigTree

:: MORE INFORMATION

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ProtASR 2.2 – Ancestral Sequence Reconstruction of Proteins accounting for Structural Constraints

ProtASR 2.2

:: DESCRIPTION

ProtASR is an evolutionary framework to reconstruct ancestral protein sequences accounting for structural constraints.

::DEVELOPER

Dr. Miguel Arenas

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ProtASR

:: MORE INFORMATION

Citation

Arenas M, Bastolla U.
ProtASR2: Ancestral reconstruction of protein sequences accounting for folding stability.
Methods Ecol Evol. 2020; 11: 248–257. https://doi.org/10.1111/2041-210X.13341

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

ProtEvol 1.0 – Maximum Likelihood Phylogenetic Inference with Selection on Protein Folding Stability

ProtEvol 1.0

:: DESCRIPTION

The program ProtEvol performs two kinds of computation.

  1. It computes the mean-field site-specific amino acid distributions that have minimal differences with respect to the background distribution and that constraint the average stability of the native state of the protein against both unfolding and misfolding. The program also computes an exchangeability matrix derived from an empirical substitution model or from a mutation model that can be used together with the site-specific distributions for applications in phylogenetic inference.
  2. It simulates protein evolution subject to the constraint of selection on the folding stability of the native state of the protein against both unfolding and misfolding.

::DEVELOPER

Unidad de Bioinformatica CBMSO

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  ProtEvol

:: MORE INFORMATION

Citation

Maximum likelihood phylogenetic inference with selection on protein folding stability.
Arenas M, Sánchez-Cobos A, Bastolla U.
Mol Biol Evol. 2015 Apr 2. pii: msv085.

SeaView 5.0.5 – Sequence Alignment and Phylogenetic Tree Building

SeaView 5.0.5

:: DESCRIPTION

SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.

::DEVELOPER

PRABI-Doua

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux

:: DOWNLOAD

 SeaView

:: MORE INFORMATION

Citation

Gouy M., Guindon S. & Gascuel O. (2010)
SeaView version 4 : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building.
Molecular Biology and Evolution 27(2):221-224.

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.

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