CoevDB – Database of Pair-wise Nucleotide Coevolution

CoevDB

:: DESCRIPTION

CoevDB is a database that collects prediction of coevolution between pairs of sites within DNA coding sequences.

::DEVELOPER

The Computational Phylogenetics group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2019 Jan 8;47(D1):D50-D54. doi: 10.1093/nar/gky986.
CoevDB: a database of intramolecular coevolution among protein-coding genes of the bony vertebrates.
Meyer X, Dib L, Salamin N.

CMCpy 0.2 – Genetic Code-Message Coevolution in Python

CMCpy 0.2

:: DESCRIPTION

CMCpy provides an object-oriented python API, together with command-line interface executables, that implement “Code-Message Coevolution” models. These published evolutionary models pertain to the evolution by natural selection of a genetic code in coevolution with a population of protein-coding genes.

::DEVELOPER

Ardell Lab @ UC Merced

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 CMCpy

:: MORE INFORMATION

Citation

Evol Bioinform Online. 2013;9:111-25. doi: 10.4137/EBO.S11169. Epub 2013 Feb 27.
CMCpy: Genetic Code-Message Coevolution Models in Python.
Becich PJ1, Stark BP, Bhat HS, Ardell DH.

BIS – Analysis of the Coevolution of Amino-acid Fragments in Proteins

BIS

:: DESCRIPTION

BIS (Blocks In Sequences)is a tool for the analysis of the coevolution of amino-acid fragments in proteins, and for the identification of their networks

::DEVELOPER

Laboratory of Computational and Quantitative Biology(LCQB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Perl
  • Java
  • PhyML

:: DOWNLOAD

 BIS

:: MORE INFORMATION

Citation

L.Dib, A.Carbone,
Protein fragments: functional and structural roles of their coevolution networks,
PLoS ONE, 7(11): e48124, 2012.

Coala 1.2.1 – COevolution Assessment by a Likelihood-free Approach

Coala 1.2.1

:: DESCRIPTION

Coala is an algorithm for estimating the frequency of the events based on an approximate Bayesian computation approach.

::DEVELOPER

ERABLE (European Research team in Algorithms and Biology, formaL and Experimental)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Java

:: DOWNLOAD

 Coala

:: MORE INFORMATION

Citation

C. Baudet, B. Donati, B. Sinaimeri, P. Crescenzi, C. Gautier, C. Matias, and M.-F. Sagot.
Cophylogeny reconstruction via an approximate Bayesian computation.
Systematic Biology, 2014, doi:10.1093/sysbio/syu129.

MISTIC – Mutual Information Server to Infer Coevolution

MISTIC

:: DESCRIPTION

MISTIC is a web server for graphical representation of the information contained within a MSA (multiple sequence alignment) and a complete analysis tool for Mutual Information networks in protein families.

::DEVELOPER

Structural Bioinformatics Unit, Fundación Instituto Leloir

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W8-14. doi: 10.1093/nar/gkt427. Epub 2013 May 28.
MISTIC: Mutual information server to infer coevolution.
Simonetti FL1, Teppa E, Chernomoretz A, Nielsen M, Marino Buslje C.

CoMap 1.4.1 – Map Substitutions on a Phylogeny and Detect Coevolution

CoMap 1.4.1

:: DESCRIPTION

CoMap performs two kinds of tasks:

(Weighted) Probabilistic substitution mapping – Compute all (weighted) number of substitutions occurring on each branch of a tree, for each site of an alignment.
Co-evolution analysis – Using the substitution mapping, look for significantly groups of sites departing the null hypothesis of independence. Two kind of analyzes are provided: a pairwise analysis, presented in Dutheil et al. (2005), and a clustering analysis in Dutheil and Galtier (2007). In both cases, a parametric bootstrap approach is used to evaluate the significance of groups. Simulation results are written to separate files, a statistics software like R is required to look for the significance.

::DEVELOPER

Dr Julien Y. Dutheil

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Bio++

:: DOWNLOAD

CoMap

:: MORE INFORMATION

Cite the following article if you use the pairwise method:

Dutheil J, Pupko T, Jean-Marie A, Galtier N.
A model-based approach for detecting coevolving positions in a molecule.
Mol Biol Evol. 2005 Sep;22(9):1919-28.

Cite the following article if you use the clustering method:

Dutheil J, Galtier N.
Detecting groups of co-evolving positions in a molecule: a clustering approach.
BMC Evol Biol. 2007 Nov 30;7(1):242

Cite the following article if you use the candidate approach method:

Dutheil JY, Jossinet F, Westhof E.
Base pairing constraints drive structural epistasis in ribosomal RNA sequences.
Mol Biol Evol. 2010 Aug;27(8):1868-76

CAPS 1.0 – Coevolution Analysis using Protein Sequences

CAPS 1.0

:: DESCRIPTION

CAPS (Coevolution Analysis using Protein Sequences) is a PERL based software that identifies co-evolution between amino acid sites. Blosum-corrected amino acid distances are used to identify amino acid co-variation. The phylogenetic sequence relationships are used to remove the phylogenetic and stochastic dependencies between sites. The 3D protein structure is used to identify the nature of the dependencies between co-evolving amino acid sites.

CAPS Online Version

::DEVELOPER

Dr Mario Fares 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl

:: DOWNLOAD

 CAPS

:: MORE INFORMATION

Citation

CAPS: coevolution analysis using protein sequences.
Fares MA, McNally D.
Bioinformatics. 2006 Nov 15;22(22):2821-2. Epub 2006 Sep 27.

MatrixMatchMaker 20121201 – Predicts interacting proteins using Coevolution

MatrixMatchMaker 20121201

:: DESCRIPTION

MatrixMatchMaker or MMM predicts interacting proteins using coevolution

MMM Web Server

::DEVELOPER

The Tillier Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MatrixMatchMaker

:: MORE INFORMATION

Citation:

The Human Protein Coevolution Network
Tillier, E. R. M and R. L Charlebois,
Genome Res. 2009 Oct;19(10):1861-71.

A new, fast algorithm for detecting protein coevolution using Maximum Similar Cliques
Rodionov, A., Bezginov, A, Rose, J. and Tillier E. R. M,
Algorithms Mol Biol. 2011 Jun 14;6:17.

Coevolution reveals a network of human proteins originating with multicellularity.
Bezginov A, Clark GW, Charlebois RL, Dar VU, Tillier ER.
Mol Biol Evol. 2013 Feb;30(2):332-46. doi: 10.1093/molbev/mss218. Epub 2012 Sep 12.

Coevolution – Coevolution Analysis of Protein Residues

Coevolution

:: DESCRIPTION

Coevolution , an integrated online system that enables comparative analyses of residue coevolution with a comprehensive set of commonly used scoring functions, including Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset Variation (ELSC), mutual information and correlation-based methods.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Coevolution

:: MORE INFORMATION

Citation:

Kevin Y. Yip, Prianka Patel, Philip M. Kim, Donald M. Engelman, Drew McDermott and Mark Gerstein
An Integrated System for Studying Residue Coevolution in Proteins
Bioinformatics (2008) 24 (2): 290-292.