ConPlex – Evolutionary Analysis of Protein Complex Structure

ConPlex

:: DESCRIPTION

ConPlex is a web application for evolutionary analysis of protein complex structures. With given protein complex structures, ConPlex automatically identifies protein interfaces and carries out evolutionary conservation analyses for the identified regions.

::DEVELOPER

Structural Bioinformatics Laboratory, Pohang University of Science and Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W450-6. doi: 10.1093/nar/gkq328. Epub 2010 Apr 30.
ConPlex: a server for the evolutionary conservation analysis of protein complex structures.
Choi YS1, Han SK, Kim J, Yang JS, Jeon J, Ryu SH, Kim S.

BEAST 1.10.4 / BEAST2 2.6.1 – Bayesian Evolutionary Analysis of Molecular Sequences

BEAST 1.10.4 / BEAST2 2.6.1

:: DESCRIPTION

BEAST (Bayesian Evolutionary Analysis Samling Trees) is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.

BEAST 2 is an open source cross-platform program for Bayesian MCMC phylogenetic analysis of molecular sequences.

::DEVELOPER

The University of Auckland Computational Evolution Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java

:: DOWNLOAD

BEAST /BEAST2

:: MORE INFORMATION

Citation:

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.
Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, De Maio N, Matschiner M, Mendes FK, Müller NF, Ogilvie HA, du Plessis L, Popinga A, Rambaut A, Rasmussen D, Siveroni I, Suchard MA, Wu CH, Xie D, Zhang C, Stadler T, Drummond AJ.
PLoS Comput Biol. 2019 Apr 8;15(4):e1006650. doi: 10.1371/journal.pcbi.1006650.

Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration.
Gavryushkina A, Welch D, Stadler T, Drummond AJ.
PLoS Comput Biol. 2014 Dec 4;10(12):e1003919. doi: 10.1371/journal.pcbi.1003919.

Alexei J Drummond and Andrew Rambaut
BEAST: Bayesian evolutionary analysis by sampling trees
BMC Evolutionary Biology 2007, 7:214doi:10.1186/1471-2148-7-214

POPBAM 0.4b / POPBAMTools – Tools for Evolutionary Analysis of Short Read Sequence Alignments

POPBAM 0.4b / POPBAMTools

:: DESCRIPTION

The POPBAM software is comprehensive set of computational tools for evolutionary analysis of whole-genome alignments consisting of multiple individuals, from multiple populations or species.

POPBAMTools is an R package for reading and annotating output from popbam

::DEVELOPER

Laboratory for Comparative Population Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler / R

:: DOWNLOAD

 POPBAM , POPBAMTools

:: MORE INFORMATION

Citation

Evol Bioinform Online. 2013 Sep 1;9:343-53. doi: 10.4137/EBO.S12751. eCollection 2013.
POPBAM: Tools for Evolutionary Analysis of Short Read Sequence Alignments.
Garrigan D

mesquite 3.0.3 – Modular System for Evolutionary Analysis

mesquite 3.0.3

:: DESCRIPTION

Mesquite is software for evolutionary biology, designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed.

::DEVELOPER

Mesquite team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX

:: DOWNLOAD

mesquite

:: MORE INFORMATION

Citation

W P Maddison, D R Maddison
Mesquite: A modular system for evolutionary analysis
Evolution (2008) Volume: 62, Issue: 5,Pages: 1103-1118

Topali 2.5 r391 – Statistical & Evolutionary Analysis of Multiple Sequence Alignments

Topali 2.5 r391

:: DESCRIPTION

Topali (tree TOPology-related analysis of ALignments Interface) is a software for statistical and evolutionary analysis of multiple sequence alignments.The extended TOPALi v2 provides phylogenetic model selection, Bayesian analysis (BA) and Maximum Likelihood (ML) phylogenetic tree estimation, detection of sites under positive selection, and recombination breakpoint location analysis.

::DEVELOPER

Information & Computational Sciences, The James Hutton Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX

:: DOWNLOAD

 Topali

:: MORE INFORMATION

Citation

Milne I, Lindner D, Bayer M, Husmeier D, McGuire G, Marshall DF and Wright F (2008),
TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops,
Bioinformatics 25 (1), 126-127.

Count 10.04 – Evolutionary Analysis of Phylogenetic Profiles and Other Numerical Characters

Count 10.04

:: DESCRIPTION

Count is a software package for the evolutionary analysis of homolog family sizes (phylogenetic profiles), or other numerical census-type characters along a phylogeny. The principal data consist of the distribution of homolog family sizes across multiple genomes: for each (gene) family, that table gives the number of homologs identified in each genome.

::DEVELOPER

Miklós Csűrös.

:: SCREENSHOTS

Count

:: REQUIREMENTS

  • MacOsX / Linux /Windows
  • Java

:: DOWNLOAD

  Count

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Aug 1;26(15):1910-2. doi: 10.1093/bioinformatics/btq315. Epub 2010 Jun 15.
Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood.
Csurös M.

SatDNA Analyzer 1.2 – Satellite-DNA Evolutionary Analysis

SatDNA Analyzer 1.2

:: DESCRIPTION

satDNA Analyzer is a tool devoted to the classification of Strachan Transition States in samples of satellite DNA.

::DEVELOPER

DiCITS | Distributed Computational Intelligence and Time Series

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows

:: DOWNLOAD

 SatDNA Analyzer

:: MORE INFORMATION

Citation:

Bioinformatics. 2007 Mar 15;23(6):767-8. Epub 2007 Jan 22.
SatDNA Analyzer: a computing tool for satellite-DNA evolutionary analysis.
Navajas-Pérez R, Rubio-Escudero C, Aznarte JL, Rejón MR, Garrido-Ramos MA.

PhyloStrat 1.0 – Evolution Simulation Software for Evolutionary Analysis

PhyloStrat 1.0

:: DESCRIPTION

PhyloStrat lets the user explore what happens when species are independently designed versus evolved by descent with modification.

::DEVELOPER

Jon C. Herron

:: SCREENSHOTS

PhyloStrat

:: REQUIREMENTS

  • MacOsX / Windows 

:: DOWNLOAD

 PhyloStrat

:: MORE INFORMATION