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Co-evolving residue prediction software tools | Protein structure data analysis

Coevolution (covariation/correlated mutation) is the change of a biological object triggered by the change of a related object. For example, the coding genes of some interacting proteins are preserved or eliminated together in new species…
cooccurNet
Desktop

cooccurNet

Facilitates easy use of the co-occurrence network model. cooccurNet includes…

Facilitates easy use of the co-occurrence network model. cooccurNet includes functionalities of constructing and analyzing co-occurrence networks, as well as calculating the extent of co-occurrence…

MirrorTree
Web

MirrorTree

Allows to investigate the co-evolution of two protein families possible…

Allows to investigate the co-evolution of two protein families possible interactions and functional relationships in a taxonomic context. MirrorTree includes the possibility of starting from single…

CoPAP
Web
Desktop

CoPAP Co-evolution of Presence-Absence Patterns

A package for accurate inference of coevolving characters as manifested by…

A package for accurate inference of coevolving characters as manifested by co-occurring gains and losses. CoPAP uses state-of-the-art probabilistic methodologies to infer coevolution and allows for…

i-COMS
Web

i-COMS interprotein COrrelated Mutations Server

A web application to calculate correlated mutations between proteins. I-COMS…

A web application to calculate correlated mutations between proteins. I-COMS allows to estimate covariation between residues of different proteins by four different covariation methods. It provides a…

Phylogene
Web

Phylogene

Provides intuitive and user-friendly platform to query the patterns of…

Provides intuitive and user-friendly platform to query the patterns of conservation across 86 animal, fungal, plant and protist genomes. A protein query can be submitted either by selecting the name…

BIS2Analyzer
Web

BIS2Analyzer

Provides to the scientific community a method for the co-evolution analysis of…

Provides to the scientific community a method for the co-evolution analysis of very few and highly conserved sequences. BIS2Analyzer conveys an automatic, detailed and highly customizable, pipeline.…

pMT
Desktop

pMT

A method for associating confidence estimators (P values) to the…

A method for associating confidence estimators (P values) to the tree-similarity scores, using a null model specifically designed for the tree comparison problem. pMT largely improves the quality and…

CoeViz
Web

CoeViz

A web-based tool that provides a versatile analysis and visualization of…

A web-based tool that provides a versatile analysis and visualization of pairwise coevolution of amino acid residues. CoeViz computes three covariance metrics: mutual information, chi-square…

MISTIC
Web

MISTIC Mutual Information Server to Infer Coevolution

A complete web tool that aims to estimate the mutual coevolutionary…

A complete web tool that aims to estimate the mutual coevolutionary relationship between two residues in a protein family using corrected mutual information (MI). Correlations between positions in a…

CoEv
Desktop

CoEv

Identifies coevolving positions and their associated profile in DNA sequences…

Identifies coevolving positions and their associated profile in DNA sequences while incorporating the underlying phylogenetic relationships. CoEv is able to discriminate between coevolving and…

CAPS
Desktop
Web

CAPS Coevolution Analysis using Protein Sequences

A program that performs coevolution analysis using protein sequences, i.e. it…

A program that performs coevolution analysis using protein sequences, i.e. it searches through a set of homologous sequences and detects groups of amino acids that evolve together. The results can…

plmDCA
Desktop

plmDCA pseudolikelihood maximization Direct-Coupling Analysis

Separates direct from indirect interactions in the context of protein…

Separates direct from indirect interactions in the context of protein sequences. plmDCA was applied to 21-state Potts models describing the statistical properties of families of evolutionarily…

CS-PSeq-Gen
Desktop

CS-PSeq-Gen

Performs simulations of the evolution of protein sequences under the…

Performs simulations of the evolution of protein sequences under the constraints of a reconstructed phylogeny. CS-PSeq-Gen allows simulations to take into account the "root sequence" that…

co-evo
Algorithm

co-evo

Allows identification of co-evolved protein residues and DNA bases. co-evo…

Allows identification of co-evolved protein residues and DNA bases. co-evo demonstrates the principle of co-evolutionary relationship thanks to the basic helix-loop-helix (bHLH), Homeo, high-mobility…

Coevolution
Desktop
Web

Coevolution

Enables coevolution analysis of protein residues with a comprehensive set of…

Enables coevolution analysis of protein residues with a comprehensive set of commonly used scoring functions, including Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset Variation…

InterMap3D
Web

InterMap3D

Predicts co-evolving protein residues and plots them on the 3D protein…

Predicts co-evolving protein residues and plots them on the 3D protein structure. Starting with a single protein sequence, InterMap3D automatically finds a set of homologous sequences, generates an…

MaxSubTree
Desktop

MaxSubTree

Detects coevolved amino acid networks in protein families of variable…

Detects coevolved amino acid networks in protein families of variable divergence. MaxSubTree captures the transition along the time scale evolution of a conserved position to a coevolved position,…

QuatIdent
Web

QuatIdent Quaternary Identifier

An ensemble identifier developed by fusing the functional domain and sequential…

An ensemble identifier developed by fusing the functional domain and sequential evolution information. QuatIdent is a 2-layer predictor. The 1st layer is for identifying a query protein as belonging…

BIS
Desktop

BIS Blocks In Sequences

Analyses the coevolution of amino-acid fragments in proteins and for detecting…

Analyses the coevolution of amino-acid fragments in proteins and for detecting networks of fragments interaction. BIS allows detecting similarities in the evolutionary behavior of alignment positions…

OUNRES
Desktop

OUNRES Optimized UNited RESidue Score

Provides an optimized united residue score method.

Provides an optimized united residue score method.

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