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Variant functional prediction software tools | Whole-genome sequencing data analysis

Modern sequencing technologies produce increasingly detailed data on genomic variation. However, conventional methods for relating either individual variants or mutated genes to phenotypes present known limitations given the complex, multigenic…
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MutationTaster
Web

MutationTaster

A free, web-based application for rapid evaluation of the disease-causing…

A free, web-based application for rapid evaluation of the disease-causing potential of DNA sequence alterations. MutationTaster integrates information from different biomedical databases and uses…

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dbNSFP
Dataset

dbNSFP database for nonsynonymous SNPs' functional predictions

Eases the process of filtering and prioritizing the presumably functional…

Eases the process of filtering and prioritizing the presumably functional single nucleotide variants (SNVs) from a long list of SNVs identified in a typical whole exome sequencing (WES) study. dbNSFP…

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SNPdryad
Web

SNPdryad

Predicts deleterious effect of amino acid substitutions occurred in human…

Predicts deleterious effect of amino acid substitutions occurred in human proteins. SNPdryad is a computational method that collects the orthologous protein sequences from other mammals and performs…

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EVmutation
Desktop

EVmutation

Predicts the effects of mutations while taking into account the interactions…

Predicts the effects of mutations while taking into account the interactions that occur between amino acids in proteins or bases in RNA. EVmutation predicts the relative favourability of unseen…

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PolyPhen-2
Web
Desktop

PolyPhen-2 Polymorphism Phenotyping

Predicts possible impact of an amino acid substitution on the structure and…

Predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. For a mutation, PolyPhen…

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SIFT
Web

SIFT Sorting Tolerant From Intolerant

Predicts whether an amino acid substitution affects protein function. SIFT…

Predicts whether an amino acid substitution affects protein function. SIFT prediction is based on the degree of conservation of amino acid residues in sequence alignments derived from closely related…

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PANTHER
Web

PANTHER Protein ANalysis THrough Evolutionary Relationships

A widely used online resource for comprehensive protein evolutionary and…

A widely used online resource for comprehensive protein evolutionary and functional classification, and includes tools for large-scale biological data analysis. The latest version of PANTHER, 10.0,…

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M-CAP
Web
Desktop

M-CAP Mendelian Clinically Applicable Pathogenicity

Represents a clinical pathogenicity classifier. M-CAP aims to misclassify no…

Represents a clinical pathogenicity classifier. M-CAP aims to misclassify no more than 5% of pathogenic variants while aggressively reducing the list of variants of uncertain significance. This tool…

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VEP
Web
Desktop

VEP Variant Effect Predictor

Determines the effect of your variants (SNPs, insertions, deletions, CNVs or…

Determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Simply input the…

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Hotspot3D
Desktop

Hotspot3D

Identifies such spatial hotspots (clusters) and interprets the potential…

Identifies such spatial hotspots (clusters) and interprets the potential function of variants within them. HotSpot3D is a computational tool which identifies mutation–mutation and mutation–drug…

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Eigen
Desktop

Eigen

An unsupervised spectral approach for scoring variants which does not make use…

An unsupervised spectral approach for scoring variants which does not make use of labeled training data. Eigen produces estimates of predictive accuracy for each functional annotation score, and…

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VEST
Desktop

VEST Variant Effect Scoring Tool

Allows to estimate a gene’s importance in human disease. The VEST method for…

Allows to estimate a gene’s importance in human disease. The VEST method for estimate gene importance can be applicable to missense and other bioinformatics pathogenicity predictors. It assess the…

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PROVEAN
Desktop
Web

PROVEAN Protein Variation Effect Analyzer

A software tool which predicts whether an amino acid substitution or indel has…

A software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein. PROVEAN is useful for filtering sequence variants to identify…

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Mutationassesso…
Web

Mutationassessor

Predicts the functional impact of amino-acid substitutions in proteins, such as…

Predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms. The functional impact is assessed based on evolutionary…

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PredictSNP
Web

PredictSNP

Consensus classifiers for prediction of disease-related mutations. PredictSNP1…

Consensus classifiers for prediction of disease-related mutations. PredictSNP1 offers its users a consensus score based on the output of six different amino acid-based predictors. Because of the…

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dSysMap
Web

dSysMap

Displays Human disease-related mutations on the structural interactome. Mapping…

Displays Human disease-related mutations on the structural interactome. Mapping of mutations on protein structures and on interaction interfaces allows you to visualize the region of the interactome…

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SNAP
Web

SNAP Screening for Non-Acceptable Polymorphisms

A neural-network based tool to be used for the evaluation of functional effects…

A neural-network based tool to be used for the evaluation of functional effects single amino acid substitutions in proteins. SNAP utilizes various biophysical characteristics of the substitution, as…

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DDIG-Indel
Web

DDIG-Indel Detecting disease-causing genetic variations due to indels

A support vector machine-based method to prioritize non-frameshifting indels by…

A support vector machine-based method to prioritize non-frameshifting indels by comparing disease-associated mutations with putatively neutral mutations from the 1,000 Genomes Project. The final…

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FATHMM-XF
Web
Desktop

FATHMM-XF

Allows prediction of the functional consequences of non-coding and coding…

Allows prediction of the functional consequences of non-coding and coding single nucleotide variants (SNVs). FATHMM-XF is a method consisting in an improvement over the predictor FATHMM-MKL. The…

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GERP
Desktop

GERP Genomic Evolutionary Rate Profiling

Identifies constrained elements in multiple alignments by quantifying…

Identifies constrained elements in multiple alignments by quantifying substitution deficits.

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CHASM/SNV-Box
Desktop

CHASM/SNV-Box Cancer-specific High-throughput Annotation of Somatic Mutations

A software toolkit to prioritize SNVs based on their predicted contribution to…

A software toolkit to prioritize SNVs based on their predicted contribution to tumorigenesis. CHASM includes a database of pre-computed predictive features called SNVBox that facilitates rapid…

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Condel
Web

Condel CONsensus DELeteriousness score of missense SNVs

A method to assess the outcome of non-synonymous SNVs using a consensus…

A method to assess the outcome of non-synonymous SNVs using a consensus deleteriousness score that combines various tools (MutationAssessor, FATHMM). The simplicity of Condel allows it to be easily…

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SnpEff
Desktop
Web

SnpEff

Annotates and predicts the effects of single nucleotide polymorphisms (SNPs).…

Annotates and predicts the effects of single nucleotide polymorphisms (SNPs). SnpEff features include: (1) the ability to make thousands of predictions per second; (2) the ability to add custom…

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SNPs&GO
Web

SNPs&GO

Serves to the prediction of deleterious single amino acid polymorphisms (SAPs)…

Serves to the prediction of deleterious single amino acid polymorphisms (SAPs) using protein functional annotation. The WS-SNPs&GO web server is based on support vector machines (SVM) and for a…

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MAPP
Desktop

MAPP Multivariate Analysis of Protein Polymorphism

Quantifies the physicochemical variation in each column of a multiple sequence…

Quantifies the physicochemical variation in each column of a multiple sequence alignment and calculates the deviation of candidate amino acid replacements from this variation. The greater the…

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CRAVAT
Web

CRAVAT Cancer-Related Analysis of Variants Toolkit

Performs cancer-related analysis of variants. CRAVAT returns mutation…

Performs cancer-related analysis of variants. CRAVAT returns mutation interpretations in a dynamic interactive web environment for sorting, visualizing and inferring mechanism. The software (i)…

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proBAMr
Desktop

proBAMr

Maps peptide spectrum matches (PSMs) back to genome. proBAMr consists of three…

Maps peptide spectrum matches (PSMs) back to genome. proBAMr consists of three steps. First the peptide from a PSM is mapped to corresponding protein sequence, and its starting and ending positions…

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CAPE
Web
Desktop

CAPE CellulAr dePendent dEactivating mutations predictor

Provides a scoring scheme capable of accurately recognizing deleterious…

Provides a scoring scheme capable of accurately recognizing deleterious regulatory variants on a genome-wide scale. CAPE detects cellular dependent deactivating mutations and can prioritize…

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IMHOTEP
Web

IMHOTEP Integrating Molecular Heuristics and Other Tools for Effect Prediction

Predicts the functional consequences of mutations of human pathogenetics.…

Predicts the functional consequences of mutations of human pathogenetics. IMHOTEP integrates nine popular prediction tools (PolyPhen-2, SNPs&GO, MutPred, SIFT, MutationTaster2, Mutation Assessor…

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StructMAn
Web

StructMAn Structural Mutation Annotation

A web-based tool for annotation of human and non-human (non-synonymous) single…

A web-based tool for annotation of human and non-human (non-synonymous) single nucleotide variant (nsSNVs) in the structural context. StructMAn analyzes the spatial location of the amino acid residue…

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Align-GVGD
Web

Align-GVGD

A method that combines Grantham Variation (GV) and Grantham Deviation (GD)…

A method that combines Grantham Variation (GV) and Grantham Deviation (GD) scores to predict the transactivation activity of each missense substitution. We compared our predictions against…

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GAVIN
Web

GAVIN Gene-Aware Variant INterpretation

Delivers accurate and reliable automated classification of variants for…

Delivers accurate and reliable automated classification of variants for clinical application. GAVIN classifies variants as benign, pathogenic, or a variant of uncertain significance (VUS). It is able…

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DOMINO
Web

DOMINO

Allows detection of genes associated with dominant disorders. DOMINO is based…

Allows detection of genes associated with dominant disorders. DOMINO is based on linear discriminant analysis (LDA). It can efficiently prioritize candidate genes associated with autosomal dominant…

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MutPred
Web

MutPred

A web application tool developed to classify an amino acid substitution as…

A web application tool developed to classify an amino acid substitution as disease-associated or neutral in human. In addition, MutPred predicts molecular cause of disease. The tool requires a…

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PhD-SNP
Desktop
Web

PhD-SNP Predictor of human Deleterious Single Nucleotide Polymorphisms

A method based on support vector machines (SVMs) that starting from the protein…

A method based on support vector machines (SVMs) that starting from the protein sequence information can predict whether a new phenotype derived from a nsSNP can be related to a genetic disease in…

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MutationAligner
Dataset

MutationAligner

Enables you to explore mutation hotspots identified in protein domains from…

Enables you to explore mutation hotspots identified in protein domains from more than 5000 patients across 22 cancer types. Using multiple sequence analysis, protein domain hotspots are identified by…

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PinSnps
Web

PinSnps

A practical computational pipeline to readily perform data analyses of…

A practical computational pipeline to readily perform data analyses of protein-protein interaction networks (PPINs) by using genetic and functional information mapped onto protein structures. We…

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deltaBS
Desktop

deltaBS

A sequence analysis method for predicting whether genome variation is likely to…

A sequence analysis method for predicting whether genome variation is likely to result in phenotypic differences, and an application of the method across a variety of analysis scales. Unlike…

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StSNP
Web

StSNP Structure SNP

Provides practical, user friendly access to the wealth of information related…

Provides practical, user friendly access to the wealth of information related to nsSNPs by seamlessly connecting various databases into one pipeline. Key functional and structural information along…

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SiPhy
Desktop

SiPhy

Implements rigorous statistical tests to detect bases under selection from a…

Implements rigorous statistical tests to detect bases under selection from a multiple alignment data.

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REVEL
Desktop

REVEL Rare Exome Variant Ensemble Learner

Predicts the pathogenicity of missense variants on the basis of individual…

Predicts the pathogenicity of missense variants on the basis of individual tools: MutPred, FATHMM, VEST, PolyPhen, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP, SiPhy, phyloP, and…

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KinMutRF
Desktop

KinMutRF

Identifies automatically pathogenic variants in human kinases. KinMutRF…

Identifies automatically pathogenic variants in human kinases. KinMutRF identifies disease-associated variants satisfactorily when trained and cross-validated with the 3689 human kinase variants from…

HyB_BR
Desktop

HyB_BR Hybrid BayesR

Allows users to perform simultaneous genomic prediction and quantitative trait…

Allows users to perform simultaneous genomic prediction and quantitative trait loci (QTL) mapping. Hyb_BR is developed as a hybrid algorithm which combine an Expectation-Maximisation (EM) module and…

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Frustration
Desktop

Frustration

A framework in which index frustration, quantifying unfavorable local…

A framework in which index frustration, quantifying unfavorable local interactions, is employed as a metric to investigate the effects of single-nucleotide variants. The frustration index quantifies…

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PVP
Desktop

PVP PhenomeNET Variant Predictor

Allows highly accurate genome-scale identification of causative variants…

Allows highly accurate genome-scale identification of causative variants involved in human disease. PVP is a system which annotates and prioritizes disease variants in whole exome sequencing (WES)…

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COCOS
Desktop

COCOS COdon COnsequence Scanner

Allows annotation of reading frame changes induced by stop-lost and frame-shift…

Allows annotation of reading frame changes induced by stop-lost and frame-shift variants. COCOS is a Variant Effect Predictor (VEP) plugin that captures variant induced codon alterations and presents…

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DEOGEN
Desktop

DEOGEN

Represents a novel method for variant-effect prediction that integrates…

Represents a novel method for variant-effect prediction that integrates heterogeneous sources of biological information. DEOGEN analyzes protein and variant pair by combining different levels of…

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LS-SNP/PDB
Web

LS-SNP/PDB

A web tool for genome-wide annotation of human SNPs. LS-SNP/PDB provides…

A web tool for genome-wide annotation of human SNPs. LS-SNP/PDB provides information useful for identifying amino-acid changing SNPs (nsSNPs) that are most likely to have an impact on biological…

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phyloP
Desktop

phyloP phylogenetic P-values

Computes conservation or acceleration p-values, either lineage-specific or…

Computes conservation or acceleration p-values, either lineage-specific or across all branches. phyloP was applied to multiple alignments of 36 species in the ENCODE regions and analyze patterns of…

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HOPE
Web

HOPE Have yOur Protein Explained

An easy-to-use web service that analyses the structural effects of a point…

An easy-to-use web service that analyses the structural effects of a point mutation in a protein sequence. Input your protein sequence and the mutation and HOPE will collect and combine available…

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wKinMut
Web

wKinMut

An integrated framework for the analysis and interpretation of the consequences…

An integrated framework for the analysis and interpretation of the consequences of variants in the human kinome. wKinMut web-server offers direct prediction of the potential pathogenicity of the…

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corRna
Web

corRna

Searches the mutational landscape of a given RNA sequence for mutations that…

Searches the mutational landscape of a given RNA sequence for mutations that will significantly alter the RNA's secondary structure. corRna has several potential uses. It can be used to predict…

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MuD
Web

MuD Mutation Detector

A Random Forests-based classifier that utilizes structural and sequence-derived…

A Random Forests-based classifier that utilizes structural and sequence-derived features to assess the impact of a given substitution on the protein function. MuD is unique in that user-reported…

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PATHiVAR
Web

PATHiVAR

Estimates the functional impact that mutations have over the human signalling…

Estimates the functional impact that mutations have over the human signalling network. PATHiVAR analyses VCF files, extract the deleterious mutations, locate them over the signalling pathways in the…

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Mechismo
Web

Mechismo

Enables simultaneous consideration of thousands of 3D structures and…

Enables simultaneous consideration of thousands of 3D structures and biomolecular interactions to predict rapidly mechanistic consequences for mutations and modifications. Analysis of high-throughput…

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CHISPAs
Desktop

CHISPAs Checking for Incorrect Sequence-Phenotype Assignments

A software aimed to identify the DNA variants incorrectly assigned to a…

A software aimed to identify the DNA variants incorrectly assigned to a phenotype derived from both experimental errors and natural variations; we will refer to these as incorrect sequence-phenotype…

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iFish
Web

iFish integrated Functional inference of SNVs in human

A server for assessing whether a missense mutation is pathogenic or neutral in…

A server for assessing whether a missense mutation is pathogenic or neutral in light of gene/gene family specific features and genetic evidences. iFish predicts the pathogenicity of nonsynonymous…

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yMap
Desktop

yMap

Analyses the impact of nsSNPs on protein level in yeast for the first time.…

Analyses the impact of nsSNPs on protein level in yeast for the first time. yMap provides users with the possibility to map their variant data to PTM containing residues and protein functional…

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PANTHER-PSEP
Web
Desktop

PANTHER-PSEP PANTHER position-specific evolutionary preservation

A software tool for predicting non-synonymous genetic variants that may play a…

A software tool for predicting non-synonymous genetic variants that may play a causal role in human disease. Several previous variant pathogenicity prediction methods have been proposed that quantify…

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PriVar
Desktop

PriVar

A cross-platform Java application toolkit to prioritize variants (SNVs and…

A cross-platform Java application toolkit to prioritize variants (SNVs and InDels) from exome or whole genome sequencing data by using different filtering strategies and information of external…

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MEGA-MD
Desktop
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FATHMM-indel
Web

FATHMM-indel Functional analysis through hidden Markov models indel

Discovers and analyzes differences in non-coding mutation loads across…

Discovers and analyzes differences in non-coding mutation loads across populations. FATHMM-indel is an integrative computational model for predicting indel pathogenicity. It can be useful to…

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DMDtoolkit
Desktop

DMDtoolkit

Visualizes the structure and predicts the functional changes of mutated…

Visualizes the structure and predicts the functional changes of mutated dystrophin protein. DMDtoolkit also assists statistical prediction for clinical phenotypes. It improves the accuracy of…

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GESPA
Desktop

GESPA GEnomic Single nucleotide Polymorphism Analyzer

Predicts the pathogenicity and disease phenotype of nsSNPs. GESPA is a…

Predicts the pathogenicity and disease phenotype of nsSNPs. GESPA is a user-friendly software package for classifying disease association of nsSNPs. It allows flexibility in acceptable input formats…

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GENESIS
Web

GENESIS

Provides a cloud-based system that allows users to directly process and analyze…

Provides a cloud-based system that allows users to directly process and analyze next-generation sequencing (NGS) data through a user-friendly graphical user interface (GUI). The first objectives of…

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Mutation3D
Web

Mutation3D

A functional prediction and visualization tool for studying the spatial…

A functional prediction and visualization tool for studying the spatial arrangement of amino acid substitutions on protein models and structures. Mutation3D is intended to be used to identify…

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DoriTool
Desktop

DoriTool

Maximizes the reproducibility and research timelines, reduces the working time…

Maximizes the reproducibility and research timelines, reduces the working time of the researchers. DoriTool combines different bioinformatics algorithms and public databases to perform a complete…

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ASSEDA
Web

ASSEDA

Predicts the effects of sequence changes that alter mRNA splicing in human…

Predicts the effects of sequence changes that alter mRNA splicing in human diseases. ASSEDA evaluates changes in splice site strength based on information theory-based models of donor and acceptor…

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CAROL
Desktop

CAROL Combined Annotation scoRing toOL

A combined functional annotation score of non-synonymous coding variants. CAROL…

A combined functional annotation score of non-synonymous coding variants. CAROL combines information from PolyPhen-2 and SIFT. We use a weighted Z method to derive the combined score. We calibrate…

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HMMvar
Desktop

HMMvar

A quantitative prediction method to predict the effect of genetic variation,…

A quantitative prediction method to predict the effect of genetic variation, both indels and SNPs, using hidden Markov models. Results show that HMMvar can achieve good performance in identifying…

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G23D
Web

G23D Genomic position mapping to 3D data

A tool for conversion of human genomic coordinates to protein coordinates and…

A tool for conversion of human genomic coordinates to protein coordinates and protein structures. G23D allows mapping of genomic positions/variants on evolutionary related (and not only identical)…

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SpliceCenter
Web

SpliceCenter

Allows investigation the impact of splice variation on the interpretation of…

Allows investigation the impact of splice variation on the interpretation of data derived from those technologies. SpliceCenter provides analysis of RT-PCR primer/probe sets, effectors of RNAi,…

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VarMod
Web

VarMod Variant Modeller

Utilises both protein sequence and structural features to predict nsSNVs that…

Utilises both protein sequence and structural features to predict nsSNVs that alter protein function. VarMod develops recent observations that functional nsSNVs are enriched at protein–protein…

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NECTAR
Web

NECTAR Non-synonymous Enriched Coding muTation Archive

A database and web application to annotate disease-related and functionally…

A database and web application to annotate disease-related and functionally important amino acids in human proteins. A number of tools are available to facilitate the interpretation of DNA variants…

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ENTPRISE
Web

ENTPRISE ENTropy and PRedIcted protein StructurE

An algorithm for predicting human disease-associated amino acid substitutions…

An algorithm for predicting human disease-associated amino acid substitutions from sequence entropy and predicted protein structures. ENTPRISE is a boosted tree regression machine-learning approach…

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MutaNET
Desktop

MutaNET

Allows to measure the impact of a gene mutations in antibiotic resistance (AR)…

Allows to measure the impact of a gene mutations in antibiotic resistance (AR) genes and their potential effect on AR of bacterial strains. MutaNET enables statistical analysis on different places in…

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SpiCoDyn
Desktop

SpiCoDyn

Characterizes the spiking and bursting properties of large-scale neuronal…

Characterizes the spiking and bursting properties of large-scale neuronal networks. SpiCoDyn contains features for: i) conversion and pre-processing of raw data; ii) statistical analysis of the…

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ActiveDriverDB
Dataset

ActiveDriverDB

Permits to visualize genome mutations in gene and protein networks.…

Permits to visualize genome mutations in gene and protein networks. ActiveDriverDB proposes example queries of well-annotated genes and browse lists of disease genes with significantly enriched…

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SNPDelScore
Desktop

SNPDelScore

Determines deleterious effects of noncoding mutations. SNPDelScore is a tool…

Determines deleterious effects of noncoding mutations. SNPDelScore is a tool based on several other methods quantifying the deleteriousness of noncoding mutations (thanks to deep learning, artificial…

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ISVS
Web

ISVS Iterative Sequencing and Variant Screening

Detects genetic variants causing autosomal recessive (AR) diseases. ISVS is…

Detects genetic variants causing autosomal recessive (AR) diseases. ISVS is based on iterative cycles of gene sequencing combined with focused mutation screening. It enables user to test the…

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MAPPIN
Desktop
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POLG…
Web

POLG Pathogenicity Prediction Server

Support the diagnosis of possible POLG-related mitochondrial dysfunction. POLG…

Support the diagnosis of possible POLG-related mitochondrial dysfunction. POLG Pathogenicity Prediction Server consists in a comprehensive, interactive database providing a mutation query interface…

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ALoFT
Desktop

ALoFT Annotation of Loss-of-Function Transcripts

Allows users to annotate and predict the disease-causing potential of loss of…

Allows users to annotate and predict the disease-causing potential of loss of function (LoF) variants. ALoFT is composed of three mains characteristics: (i) functional domain annotations, (ii)…

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GeMSTONE
Web

GeMSTONE Germline Mutation Scoring Tool fOr Next-Generation sEquencing data

Allows an accessible, collaborative, replicable and holistic analysis of…

Allows an accessible, collaborative, replicable and holistic analysis of genetic variants. GeMSTONE permits to eliminate the time and space burdens associated with modern variant analysis tools. It…

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DeepEVS
Web

DeepEVS Deep Ensemble Variation Score

Integrates predictions of several popular scores (SIFT, Polyphen-2, LRT,…

Integrates predictions of several popular scores (SIFT, Polyphen-2, LRT, MutationTaster, MutationAssessor, FATHMM, PROVEAN, MetaSVM, MetaLR, GERP++, phyloP, phastCons, SiPhy) and population data to…

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Interactome INSIDER
Web
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Structure-PPi
Desktop
Web

Structure-PPi

Offers several functionalities to explore the consequence of protein mutations.…

Offers several functionalities to explore the consequence of protein mutations. It reports features that overlap the mutations, or that are in close physical proximity. The features reported include…

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MitImpact
Dataset

MitImpact Mitochondrial mutation Impact

A collection of pre-computed pathogenicity predictions for all nucleotide…

A collection of pre-computed pathogenicity predictions for all nucleotide changes that cause non-synonymous substitutions in human mitochondrial protein coding genes. MitImpact presents itself as a…

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FATHMM
Desktop
Web

FATHMM Functional Analysis through Hidden Markov Models

A high-throughput web-server capable of predicting the functional consequences…

A high-throughput web-server capable of predicting the functional consequences of both coding variants, i.e. non-synonymous single nucleotide variants (nsSNVs), and non-coding variants. To facilitate…

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NetDiseaseSNP
Web

NetDiseaseSNP

A sequence conservation-based artificial neural network predictor which…

A sequence conservation-based artificial neural network predictor which classifies nsSNPs as disease-causing or neutral. NetDiseaseSNP uses the alignment generation algorithm of SIFT to identify…

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PON-P2
Web

PON-P2

A powerful tool for screening harmful variants and for ranking and prioritizing…

A powerful tool for screening harmful variants and for ranking and prioritizing experimental characterization. PON-P2 is a machine learning-based classifier and groups the variants into pathogenic,…

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HPMV
Web

HPMV Human Protein Mutation Viewer

Relates human protein sequence mutations to sequence architectural features and…

Relates human protein sequence mutations to sequence architectural features and to study their influence on mechanistic, segment-specific functional properties of proteins. The HPMV is an efficient…

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mCSM-lig
Web

mCSM-lig

A structure-guided computational approach for quantifying the effects of…

A structure-guided computational approach for quantifying the effects of single-point missense mutations on affinities of small molecules for proteins. mCSM-lig uses graph-based signatures to…

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PinPor
Web
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HMMvar-func
Desktop

HMMvar-func

A method for predicting the functional outcome of mutations in coding regions.…

A method for predicting the functional outcome of mutations in coding regions. The fine grained prediction provides richer information than current existing tools that can be especially useful for…

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PaPI
Web

PaPI

A machine-learning approach to classify and score human coding variants by…

A machine-learning approach to classify and score human coding variants by estimating the probability to damage their protein-related function. PaPI combines Pseudo Amino Acid Composition (PseAAC),…

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Shannon…
Web

Shannon pipeline

A software tool for genome-scale mutation analysis and predicts variants…

A software tool for genome-scale mutation analysis and predicts variants affecting mRNA splicing. Individual information contents (in bits) of reference and variant splice sites are compared and…

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EFIN
Desktop
Web

EFIN Evaluation of Functional Impact of Nonsynonymous SNPs

Predicts whether amino acids substitution would related to disease evaluated by…

Predicts whether amino acids substitution would related to disease evaluated by random forests based on protein conservation. Testing of this algorithm on a comprehensive dataset showed significant…

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prfreq
Desktop

prfreq

Uses Poisson random fields to calculate expected allele frequency distributions…

Uses Poisson random fields to calculate expected allele frequency distributions under various possible distributions of selective effects and demographic models. prfreq estimates demography and a…

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GS3
Desktop

GS3 Genomic Selection --- Gibbs Sampling --- Gauss Seide

Serves for genome-wide genetic evaluations and validations. GS3 allows to…

Serves for genome-wide genetic evaluations and validations. GS3 allows to realize genomic prediction and genome data analysis. This tool estimates effects of single nucleotide polymorphism (SNPs)…

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MutationMotif
Desktop

MutationMotif

A package for analysis of mutation properties. Two different analysis…

A package for analysis of mutation properties. Two different analysis approaches are supported: (1) log-linear analysis of neighbourhood base influences on mutation coupled with a sequence logo like…

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DMDM
Dataset

DMDM Domain Mapping of Disease Mutations

Provides an aggregated view of all human coding disease-related mutations and…

Provides an aggregated view of all human coding disease-related mutations and SNPs for each protein domain. To build DMDM, all human proteins were aligned to a database of conserved protein domains…

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M2SG
Web

M2SG

An online database and interactive web server to (i) retrieve the mapped OMIM…

An online database and interactive web server to (i) retrieve the mapped OMIM and SwissVar variants for a given protein sequence; and (ii) obtain related proteins and mutations for an input disease…

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MuPIT interactive
Web

MuPIT interactive Mutation position imaging toolbox interactive

A browser-based application for single-nucleotide variants (SNVs), which…

A browser-based application for single-nucleotide variants (SNVs), which automatically maps the genomic coordinates of SNVs onto the coordinates of available three-dimensional (3D) protein…

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mCluster
Web

mCluster

Represents an approach to identifying and elucidating protein mutations with…

Represents an approach to identifying and elucidating protein mutations with major consequences for protein function. This approach is distinct from and complementary to existing analysis methods…

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VariBench
Dataset

VariBench

A benchmark database suite comprising variation datasets for testing and…

A benchmark database suite comprising variation datasets for testing and training methods for variation effect prediction. VariBench contains information for experimentally verified effects and…

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SuSPect
Web
Desktop

SuSPect disease-SUsceptibility-based Single amino acid variant phenotype PrEdiCTion

Recognizes disease-associated single amino acid variants (SAVs). SuSPect…

Recognizes disease-associated single amino acid variants (SAVs). SuSPect combines sequence and structural features with several other characteristics including network information to train a support…

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MICO
Web

MICO Mutation Information COllector

Presents an unbiased view of all possible predictions on the effects of a given…

Presents an unbiased view of all possible predictions on the effects of a given mutation. MICO is a web application that contains six leading prediction tools: Condel, MutationAssesor, Mutation…

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KaKs Calculator
Desktop

KaKs Calculator

Calculates nonsynonymous (Ka) and synonymous (Ks) substitution rates through…

Calculates nonsynonymous (Ka) and synonymous (Ks) substitution rates through model selection and model averaging. KaKs Calculator implements a set of candidate models in a maximum likelihood…

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Simprot
Web
Desktop

Simprot

Simulates protein sequence evolution with the additional capability of being…

Simulates protein sequence evolution with the additional capability of being able to simulate insertions and deletions (indels) with a variable length distribution. Simprot allows the protein…

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CoVEC
Web
Desktop

CoVEC Consensus Variant Effect Classification

Integrates prediction whether non-synonymous variants are neutral or…

Integrates prediction whether non-synonymous variants are neutral or disease-causing from four methods. CoVEC offers a way to draw a consensus out of the prediction of four independent 3rd-party…

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RNA Sequence…
Web

RNA Sequence Mutation

Mutates the nucleobase identity to the specified sequence into the furnished 3D…

Mutates the nucleobase identity to the specified sequence into the furnished 3D structure. RNA Sequence Mutation is a method available via a web interface. It can be useful to perform point mutations…

NSLR
Desktop

NSLR Network-regularized Sparse Logistic Regression

Incorporates clinical binary outcome, gene expression data, and normalized…

Incorporates clinical binary outcome, gene expression data, and normalized Laplacian matrix that encode protein-protein interaction (PPI) network. NSLR helps user to make biomarker discovery and…

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gene.iobio
Web

gene.iobio

Allows disease-causing variant interrogation. gene.iobio is a web-server…

Allows disease-causing variant interrogation. gene.iobio is a web-server developed to allow visualization and analysis of genetic variants. It can be used for identifying potentially interesting…

SVS
Desktop

SVS SNP and Variation Suite

Allows to perform complex analyses and visualizations on genomic and phenotypic…

Allows to perform complex analyses and visualizations on genomic and phenotypic data. SVS provides a set of tools to (1) empower quickly and easily perform quality-assurance and statistical tests for…

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PON-PS
Web

PON-PS

Predicts severity due to amino acid substitutions (AASs). PON-PS is a method…

Predicts severity due to amino acid substitutions (AASs). PON-PS is a method based on machine learning and trained on known instances. This resource distinguishes variations leading to severe…

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seqr
Web
Desktop

seqr

Allows to work with next generation sequencing (NGS) data, specifically in the…

Allows to work with next generation sequencing (NGS) data, specifically in the context of studying rare genetic diseases. Seqr is an open source web interface designed to make research productive,…

SCYPPred
Web

SCYPPred

A web-server developed for predicting human cytochrome P450 SNPs (Single…

A web-server developed for predicting human cytochrome P450 SNPs (Single Nucleotide Polymorphisms) based on the SVM flanking sequence method. SCYPPred can yield the desired results by using the amino…

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GenomeGems
Desktop

GenomeGems

Enables researchers to identify potential disease-causing SNPs in an efficient…

Enables researchers to identify potential disease-causing SNPs in an efficient manner. This enables rapid turnover of information and leads to further experimental SNP validation. GenomeGems allows…

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PyMut
Web

PyMut

Permits to design loss-of-function mutations for yeast as most of the yeast…

Permits to design loss-of-function mutations for yeast as most of the yeast genes has a very simple structure. PyMut is based on the degeneracy of genetic code and uses it to generate the…

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GREMET
Web

GREMET Gene REgulation Mutation Effect Tool

Identifies multiple functional changes inferred by single-nucleotide…

Identifies multiple functional changes inferred by single-nucleotide substitutions or indels in a reference genomic sequence. GREMET is a web application allowing detection of potential alterations…

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COPE-TFBS
Web
Desktop
Information