RADIS 1.0.0 – Analysis of RAD-seq data for InterSpecific Phylogeny

RADIS 1.0.0

:: DESCRIPTION

RADIS is a perl pipeline which makes the processing of RAD-seq data easier and allows rapid and automated exploration of parameters/data for phylogenetic inference.

::DEVELOPER

Centre de Biologie et Gestion des Populations (CBGP)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 RADIS

:: MORE INFORMATION

Citation

RADIS: Analysis of RAD-seq data for InterSpecific phylogeny.
Cruaud A, Gautier M, Rossi JP, Rasplus JY, Gouzy J.
Bioinformatics. 2016 Jun 16. pii: btw352.

Cocos – Reconstructing Phylogenies of Multi-Domain Proteins

Cocos

:: DESCRIPTION

Cocos is a tool to construct phylogenies of multi-domain proteins.

::DEVELOPER

Research Group Microbial Virulence

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

 Cocos

:: MORE INFORMATION

Citation

Cocos: Constructing multi-domain protein phylogenies.
Homilius M, Wiedenhoeft J, Thieme S, Standfuß C, Kel I, Krause R.
PLoS Curr. 2011 Jun 9;3:RRN1240. doi: 10.1371/currents.RRN1240.

PIVO 2 – Phylogeny by IteratiVe Optimization

PIVO 2

:: DESCRIPTION

PIVO is a program that reconstructs ancestral gene orders on complex phylogenies. Because it uses the DCJ model, it can handle linear, circular, and multilinear genomes. PIVO is mainly targeted at reconstructing rerrangement histories of mitochondrial genomes.

:: DEVELOPER

Computational Biology @ Comenius University in Bratislava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 PIVO

:: MORE INFORMATION

Citation

Albert Herencsár, Broňa Brejová .
An Improved Algorithm for Ancestral Gene Order Reconstruction.
In V. Kurkova, L. Bajer, V. Svatek, ed., Information Technologies – Applications and Theory (ITAT), number 1003 in CEUR-WS, pp. 46-53, Jasna, Slovakia, 2014.

DupLoCut – Duplication Loss Phylogeny by Cutting Planes

DupLoCut

:: DESCRIPTION

DupLoCut computes ancestral gene orders, given a phylogenetic tree and gene orders assigned to the leaves of the tree. It attempts to find the most parsimony assignment of gene orders under the duplication-loss evolutionary model.

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

  DupLoCut

:: MORE INFORMATION

Citation

J Comput Biol. 2013 Sep;20(9):643-59. doi: 10.1089/cmb.2013.0057.
The duplication-loss small phylogeny problem: from cherries to trees.
Andreotti S1, Reinert K, Canzar S.

TransPhylo 1.0 – Inference of Pathogen Transmission Tree given Phylogeny

TransPhylo 1.0

:: DESCRIPTION

TransPhylo is a software package for the Bayesian inference of infectious disease transmission from a phylogeny.

::DEVELOPER

Xavier Didelot

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab

:: DOWNLOAD

 TransPhylo

:: MORE INFORMATION

Citation

Mol Biol Evol. 2014 Jul;31(7):1869-79. doi: 10.1093/molbev/msu121. Epub 2014 Apr 8.
Bayesian inference of infectious disease transmission from whole-genome sequence data.
Didelot X, Gardy J, Colijn C

MrBayes 3.2.5 – Bayesian Inference of Phylogeny

MrBayes 3.2.5

:: DESCRIPTION

MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes’s theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees.

::DEVELOPER

MrBayes Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

MrBayes

:: MORE INFORMATION

Citation:

MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP.
Syst Biol. 2012 May;61(3):539-42. doi: 10.1093/sysbio/sys029.

Ronquist F, Huelsenbeck JP.
MrBayes 3: Bayesian phylogenetic inference under mixed models.
Bioinformatics. 2003 Aug 12;19(12):1572-4.

FastME 2.1.4 – Fast & Accurate Phylogeny Reconstruction

FastME 2.1.4

:: DESCRIPTION

FastME is a software for fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. FastME showed better topological accuracy than NJ, BIONJ, WEIGHBOR and FITCH, in all evolutionary conditions we tested, which include large range deviations from molecular clock and substitution rates. When the number of taxa is high, its superiority over NJ, BIONJ and WEIGHBOR becomes important, while FITCH remains close to FastME but becomes hard to use due to its slowness. FastME is very fast, even faster than NJ, and can easily be applied to very large data sets (> 1000 taxa).

::DEVELOPER

The Computational Biology Institute (IBC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX

:: DOWNLOAD

FastME

:: MORE INFORMATION

Citation

Mol Biol Evol. 2015 Oct;32(10):2798-800. doi: 10.1093/molbev/msv150. Epub 2015 Jun 30.
FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program.
Lefort V, Desper R, Gascuel O

Desper R., Gascuel O.
Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle.
Journal of Computational Biology. 2002 9(5):687-705.

CompPhy – A Web-based Collaborative Platform for comparing Phylogenies

CompPhy

:: DESCRIPTION

CompPhy is a web platform dedicated to the collaborative handling of phylogenetic trees.

:: DEVELOPER

The Computational Biology Institute (IBC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Evol Biol. 2014 Dec 14;14(1):253.
CompPhy: a web-based collaborative platform for comparing phylogenies.
Fiorini N, Lefort V, Chevenet F, Berry V, Chifolleau AM.

BAli-Phy 2.3.7 – Bayesian Alignment and Phylogeny estimation

BAli-Phy 2.3.7

:: DESCRIPTION

BAli-Phy is MCMC software for simultaneous Bayesian estimation of alignment and phylogeny (and other parameters).BAli-Phy can estimate phylogenetic trees from sequence data when the alignment is uncertain. Instead of conditioning on a single alignment estimate, BAli-Phy accounts for alignment uncertainty by integrating over all alignments. BAli-Phy does not rely on a guide tree because the alignment and the tree are co-estimated. Therefore it can construct phylogeny estimates of widely divergent sequences without bias toward a guide tree.

::DEVELOPER

Marc A. Suchard, M.D., Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows

:: DOWNLOAD

 BAli-Phy

:: MORE INFORMATION

Citation

Suchard MA and Redelings BD
BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny,
Bioinformatics, 22:2047-2048, 2006.

Chaos Game – Analyzing Phylogeny of Viral Sequences

Chaos Game

:: DESCRIPTION

Chaos Game is a program based on chaos game representation for analyzing phylogeny of viral sequences.

::DEVELOPER

Hughes Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • Perl

:: DOWNLOAD

 Chaos Game

:: MORE INFORMATION