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Gene orthology detection software tools | Comparative genomics

Accurate inference of orthologous genes is a pre-requisite for most comparative genomics studies, and is also important for functional annotation of new genomes. Identification of orthologous gene sets typically involves phylogenetic tree analysis,…
UCSC Genome Browser
Web

UCSC Genome Browser University of California Santa Cruz Genome Browser

Displays the assembled human genome and other mammalian genomes. UCSC Genome…

Displays the assembled human genome and other mammalian genomes. UCSC Genome Browser provides browsers for more than 180 assemblies and over 100 species. It provides a collection of tools to explore…

OMA
Web

OMA Orthologous MAtrix

Aims to create relations between genes across many species from all of life.…

Aims to create relations between genes across many species from all of life. OMA offers a web browser to request new or updated genomes easily. It integrates domain annotations from Gene3D for…

ParameciumDB
Dataset

ParameciumDB

Provides data about the model organism Paramecium tetraurelia. ParameciumDB was…

Provides data about the model organism Paramecium tetraurelia. ParameciumDB was created by using components of the Generic Model Organism Database (GMOD). It offers data about gene expression data…

G T A T C G C T A
BLASTP
Web

BLASTP Standard Protein BLAST

Programs search protein databases using a protein query. Algorithms: blastp,…

Programs search protein databases using a protein query. Algorithms: blastp, psi-blast, phi-blast, delta-blast.

orthAgogue
Desktop

orthAgogue

A tool for high speed estimation of homology relations within and between…

A tool for high speed estimation of homology relations within and between species in massive data sets.

primeGEM
Desktop

primeGEM

Computes for a pair of genes the probability that they are orthologous.…

Computes for a pair of genes the probability that they are orthologous. primeGEM is a program that performs probabilistic orthology analysis. This framework is based on the gene evolution model which…

OrthoReD
Desktop

OrthoReD Orthology predictions from Reduced Datasets

Represents a tree-building-based orthology prediction tool. OrthoReD can be…

Represents a tree-building-based orthology prediction tool. OrthoReD can be executed on a single gene of interest, on a subset of genes in a genome, or on all the genes in the genome. This…

DLRSOrthology
Desktop

DLRSOrthology Duplication Loss Rate and Sequence Orthology

A package to compute orthology probabilities. DLRSOrthology enables orthology…

A package to compute orthology probabilities. DLRSOrthology enables orthology inference with respect to the DLRS (Duplication, Loss, Rate and Sequence) model by extending the original PrIME-DLR…

WORMHOLE
Web

WORMHOLE WORM Human OrthoLogy Explorer

Applies machine learning to integrate 17 distinct ortholog prediction…

Applies machine learning to integrate 17 distinct ortholog prediction algorithms to identify novel least diverged orthologs (LDOs) between 6 eukaryotic species-humans, mice, zebrafish, fruit flies,…

PSAT
Web
Desktop

PSAT Prokaryotic Sequence homology Analysis Tool

Allows users to perform comparative genomics tasks. PSAT authorizes to compare…

Allows users to perform comparative genomics tasks. PSAT authorizes to compare a single reference genome with the bacterial genomes publicly available through NCBI, including selected genomes from…

pPAP
Desktop

pPAP

Predicts the reaction of a plant type III polyketide synthases (PKS). pPAP…

Predicts the reaction of a plant type III polyketide synthases (PKS). pPAP targets PKSs acting on ring-type starter substrates, and classifies their functions into four reaction types. It is based on…

ORCAN
Web

ORCAN ORtholog sCANner

A web-based meta-server for one-click evolutionary and functional annotation of…

A web-based meta-server for one-click evolutionary and functional annotation of protein sequences. ORCAN combines information from the most popular orthology-prediction resources, including 4 tools…

OGCleaner
Desktop

OGCleaner

Filters putative homology clusters of amino acid sequences by using machine…

Filters putative homology clusters of amino acid sequences by using machine learning algorithms based on annotated orthology clusters. The OGCleaner is designed for homology cluster filtering by…

G T A T C G C T A
DeNoGAP
Desktop

DeNoGAP De-Novo Genome Analysis Pipeline

Performs reference-assisted and de novo gene prediction, homolog protein family…

Performs reference-assisted and de novo gene prediction, homolog protein family assignment, ortholog prediction, functional annotation, and pan-genome analysis. DeNoGAP integrates bioinformatics…

HaMStR
Desktop

HaMStR Hidden Markov Model based Search for Orthologs using Reciprocity

Extends predefined groups of orthologous genes derived from taxa. HaMStR…

Extends predefined groups of orthologous genes derived from taxa. HaMStR exhibits a very low false positive rate (FDR) and good sensitivity. For it, a profile Hidden Markov Model (HMM) that captures…

OrthoFinder
Desktop

OrthoFinder

A program for identifying orthologous protein sequence families. Using real…

A program for identifying orthologous protein sequence families. Using real benchmark datasets we demonstrate that OrthoFinder is more accurate than other orthogroup inference methods by between 8 %…

LmCGST
Desktop

LmCGST Listeria monocytogenes Core-Genome Sequence Typer

Provides increased discriminatory power relative to typing methods such as…

Provides increased discriminatory power relative to typing methods such as pulsed-field gel electrophoresis, ribotyping, and multi-locus sequence typing while it addresses several shortcomings of…

Ortholog-Finder
Desktop

Ortholog-Finder

Helps is the construction of ortholog data sets for phylogenetic analysis.…

Helps is the construction of ortholog data sets for phylogenetic analysis. Ortholog-Finder is a program to eliminate the effects of horizontal gene transfer (HGT) genes and out-paralogs from the…

Orthonome
Dataset

Orthonome

Provides several information about Drosophila genomes. Orthonome works as a…

Provides several information about Drosophila genomes. Orthonome works as a searchable database and query tool with multiple-sequence alignment browsers for all sets of orthologues. Users can realize…

aLeaves
Dataset

aLeaves

Collects homologue from diverse animal genomes. aLeaves collects sequences…

Collects homologue from diverse animal genomes. aLeaves collects sequences similar to an input query sequence from various data sources. It provides a unique online platform to explore metazoan gene…

OrthoVenn
Web

OrthoVenn

A web platform for comparison and annotation of orthologous gene clusters among…

A web platform for comparison and annotation of orthologous gene clusters among multiple species. OrthoVenn provides comprehensive coverage of vertebrates, metazoa, protists, fungi, plants and…

OrthoANI
Desktop

OrthoANI Average Nucleotide Identity by Orthology

Provides a modified version of average nucleotide identity (ANI) to solve the…

Provides a modified version of average nucleotide identity (ANI) to solve the problem of reciprocal inconsistency of the original ANI algorithm. OrthoANI provides a measure of genomic relatedness…

OrthoMaM
Web

OrthoMaM Orthologous Mammalian Markers

A database of orthologous mammalian markers describing the evolutionary…

A database of orthologous mammalian markers describing the evolutionary dynamics of orthologous genes in mammalian genomes using a phylogenetic framework. Since its first release in 2007, OrthoMaM…

Orthograph
Desktop

Orthograph

Identifies orthologous (and paralogous) nucleotide or amino acid sequences,…

Identifies orthologous (and paralogous) nucleotide or amino acid sequences, which resolves existing algorithmic and software-technical issues. Orthograph applies a best reciprocal hit search strategy…

OrthoClust
Desktop

OrthoClust

For simultaneously clustering data across multiple species.

For simultaneously clustering data across multiple species.

Hieranoid
Desktop

Hieranoid Hierarchical Orthology Inference

Allows orthology inference. Hieranoid is an hybrid between tree and graph based…

Allows orthology inference. Hieranoid is an hybrid between tree and graph based approaches that infer groups of orthologs in a hierarchical structure. The software uses a species tree as a guide tree…

ReMark
Desktop

ReMark

Provides multiple, flexible approaches to cluster orthologous proteins. ReMark…

Provides multiple, flexible approaches to cluster orthologous proteins. ReMark is a fully automatic application that first detects and recursively clusters ortholog pairs through reciprocal BLAST…

EvoCor
Web

EvoCor

Predicts genes involved in affecting specific cellular processes together with…

Predicts genes involved in affecting specific cellular processes together with a gene of interest. EvoCor integrates profiles of sequence divergence derived by a Hidden Markov Model (HMM) and…

OrthoGNC
Desktop

OrthoGNC

Determines pairwise orthology relations. OrthoGNC first calculates pairwise…

Determines pairwise orthology relations. OrthoGNC first calculates pairwise sequence similarities, then identifies homologous sequences, for finally inferring orthologs according to gene neighborhood…

OMGene
Desktop

OMGene Optimise My Gene

Optimises the agreement between gene models for orthologous genes in multiple…

Optimises the agreement between gene models for orthologous genes in multiple species in order to improve genome annotations. OMGene aims to find the most consistent set of representative gene models…

PorthoMCL
Desktop

PorthoMCL

Facilitates comparative genomics analysis through exploiting the exponentially…

Facilitates comparative genomics analysis through exploiting the exponentially increasing number of sequenced genomes. PorthoMCL is a parallel orthology prediction tool using a Markov Clustering…

Pairup
Desktop

Pairup

Assists user in resolving the problem of matching paralogs from a pair of…

Assists user in resolving the problem of matching paralogs from a pair of proteins within a single species. Pairup is a method that is aimed at eukaryotic proteins where the number of sequences…

G2F
Dataset

G2F Gene2Function

Allows to search information about human genes or common genetic model species…

Allows to search information about human genes or common genetic model species and displays summary information for each ortholog. G2F simplifies to survey the wealth of information available for…

RecBlast
Web
Desktop

RecBlast Reciprocal Blast

Enables fast and easy discovery of orthologues along and across the…

Enables fast and easy discovery of orthologues along and across the evolutionary tree. RecBlast is capable of running heavy, large-scale and complex Reciprocal Blast comparisons across multiple genes…

FamFetch
Desktop

FamFetch

Identifies homologous genes and interprets their relationships (orthology or…

Identifies homologous genes and interprets their relationships (orthology or paralogy). The user can specify the topology of the tree pattern, and set constraints on its nodes and leaves. Then, this…

HOMECAT
Desktop

HOMECAT HOmology Mapper for Enrichment and Comparative Analysis with Translation

Allows cross-species data comparison with a particular emphasis on functional…

Allows cross-species data comparison with a particular emphasis on functional genomic data (i.e. microarrays and other high throughput biological data sources). HOMECAT aims to facilitate…

COSER
Desktop

COSER COmpare genomes with SEgmental duplications and Rearrangement

A software package to compare two arbitrary genomes in an evolutionary model…

A software package to compare two arbitrary genomes in an evolutionary model that includes both rearrangements and segmental duplications. COSER can also be applied to assign in-paralogs and…

G T A T C G C T A
BUSCO
Desktop

BUSCO Benchmarking Universal Single-Copy Orthologs

Provides measures for quantitative assessment of genome assembly, gene set, and…

Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal…

POGs2
Dataset

POGs2 Putative Orthologous Groups 2

Brings together functional and structural annotations for orthologous genes in…

Brings together functional and structural annotations for orthologous genes in a manner that simplifies cross-species comparison and functional inference. POGs2 is a database that retains the…

FAT-CAT
Web

FAT-CAT Fast Approximate Tree Classification

An approach to ortholog identification using subtree hidden Markov model-based…

An approach to ortholog identification using subtree hidden Markov model-based placement of protein sequences to phylogenomic orthology groups in the PhyloFacts database. Results on a data set of…

CLfinder-OrthNe…
Desktop

CLfinder-OrthNet

Enables detection of all orthologs that share a given evolutionary context.…

Enables detection of all orthologs that share a given evolutionary context. CLfinder-OrthNet identifies co-linearity (CL) in the arrangement of orthologous loci among multiple genomes and builds…

CAT
Desktop

CAT Comparative Annotation Toolkit

Allows comparison and separation of orthology relationships. CAT uses the…

Allows comparison and separation of orthology relationships. CAT uses the reference free duplication-aware multiple genome alignments to comment multiple genomes simultaneously and symmetrically.…

FastANI
Desktop

FastANI Fast Average Nucleotide Identity

Enables accurate estimation of pairwise Average Nucleotide Identity (ANI)…

Enables accurate estimation of pairwise Average Nucleotide Identity (ANI) values for large cohorts of genomes. FastANI is an algorithm based on alignment-free sequence mapping engine. It provides…

GeneSeqToFamily
Desktop

GeneSeqToFamily

Uses existing tools from the Galaxy ToolShed, as well as providing additional…

Uses existing tools from the Galaxy ToolShed, as well as providing additional wrappers and tools that are required to run the workflow. GeneSeqToFamily represents the Ensembl Compara pipeline as a…

DIOPT
Web

DIOPT Drosophila RNAi Screening Center Integrative Ortholog Prediction Tool

Allows rapid identification of orthologs. DIOPT integrates existing approaches,…

Allows rapid identification of orthologs. DIOPT integrates existing approaches, facilitating rapid identification of orthologs among human, mouse, zebrafish, C. elegans, Drosophila, and S.…

DIOPT-DIST
Web

DIOPT-DIST DIOPT Diseases and Traits

Maps gene-disease relationships from the NCBI Online Mendelian Inheritance in…

Maps gene-disease relationships from the NCBI Online Mendelian Inheritance in Man (OMIM) database and genome-wide association studies (GWAS) datasets contained in the GWAS catalog to genes in the C.…

OrthoInspector
Desktop

OrthoInspector

A software system incorporating an original algorithm for the rapid detection…

A software system incorporating an original algorithm for the rapid detection of orthology and inparalogy relations between different species. OrthoInspector is a database of precomputed orthology…

MultiMSOAR
Desktop

MultiMSOAR

Identifies ortholog groups among multiple genomes. MultiMSOAR provides…

Identifies ortholog groups among multiple genomes. MultiMSOAR provides information about gene births, duplications and losses in evolution, which may be of independent biological interest. It is able…

OrthoSelect
Desktop

OrthoSelect

Processes clustered expressed sequence tags (EST) sequences automatically for…

Processes clustered expressed sequence tags (EST) sequences automatically for phylogenomic studies. OrthoSelect carries out analyses on a phylogenomic scale. It integrates publicly available…

TriFusion
Desktop

TriFusion

Serves to streamline the workflow of phylogenomic projects. TriFusion aims to…

Serves to streamline the workflow of phylogenomic projects. TriFusion aims to mitigate this issue by providing a user-friendly visual interface available for users without any programming knowledge…

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