tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.

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

Offers online public access to a growing database of genomic sequence and…

Offers online public access to a growing database of genomic sequence and annotations for a large collection of organisms, primarily vertebrates, with an emphasis on the human and mouse genomes. The…

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…

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.

OMA
Web

OMA Orthologous MAtrix

A method and database for the inference of orthologs among complete genomes.…

A method and database for the inference of orthologs among complete genomes. The distinctive features of OMA are its broad scope and size, high quality of inferences, feature-rich web interface,…

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,…

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…

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…

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.

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…

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…

Hieranoid
Desktop

Hieranoid Hierarchical Orthology Inference

An orthology inference method using a hierarchical approach. Hieranoid performs…

An orthology inference method using a hierarchical approach. Hieranoid performs pairwise orthology analysis using InParanoid at each node in a guide tree as it progresses from its leaves to the root.…

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…

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…

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…

BiDiBlast
Desktop

BiDiBlast Bi-Directional BLAST

An approach to detect, annotate, and analyze candidate orthologous or…

An approach to detect, annotate, and analyze candidate orthologous or paralogous sequences in a single go. BiDiBlast submits two batches of sequences to local versions of the NCBI BLAST tool, manages…

COCO-CL
Desktop

COCO-CL

A method for hierarchical clustering of homology relations and identification…

A method for hierarchical clustering of homology relations and identification of orthologous groups of genes. Unlike previous approaches, which are based on pairwise sequence comparisons, this method…

SPOCS
Desktop
Web

SPOCS

Implements a graph-based ortholog prediction method to generate a simple…

Implements a graph-based ortholog prediction method to generate a simple tab-delimited table of orthologs.

morFeus
Web

morFeus

A search program to find remotely conserved orthologs. Based on relaxed…

A search program to find remotely conserved orthologs. Based on relaxed sequence similarity searches, morFeus selects sequences based on the similarity of their alignments to the query, tests for…

MSOAR
Desktop

MSOAR

An improved system for one-to-one ortholog assignment. For a pair of input…

An improved system for one-to-one ortholog assignment. For a pair of input genomes, the system first focuses on the tandemly duplicated genes of each genome and tries to identify among them those…

Ortholuge
Desktop

Ortholuge

Improves the specificity of ortholog identification and is suitable for…

Improves the specificity of ortholog identification and is suitable for high-throughput use. Ortholuge provides important data set evaluation for a variety of analyses based on comparative…

RIO
Desktop

RIO Resampled Inference of Orthologs

Automates phylogenomic using explicit phylogenetic inference. RIO analyses are…

Automates phylogenomic using explicit phylogenetic inference. RIO analyses are performed over bootstrap resampled phylogenetic trees to estimate the reliability of orthology assignments. It is useful…

LOFT
Desktop

LOFT Levels of Orthology From Trees

Assigns hierarchical orthology numbers to genes based on a phylogenetic tree.…

Assigns hierarchical orthology numbers to genes based on a phylogenetic tree. LOFT method also brings a new concept called “levels of orthology” to describe the multi-level nature of gene…

DODO
Desktop

DODO DOmain based Detection of Orthologs

An efficient method to detect orthologs in genomes. Supported by domain…

An efficient method to detect orthologs in genomes. Supported by domain composition, which usually directly related with protein function, DODO could facilitate orthologs detection across distantly…

Proteinortho
Desktop

Proteinortho

A stand-alone tool that is geared towards large datasets and makes use of…

A stand-alone tool that is geared towards large datasets and makes use of distributed computing techniques when run on multi-core hardware.

UCSC LiftOver
Web
Desktop

UCSC LiftOver

Converts genome coordinates and genome annotation files between assemblies.…

Converts genome coordinates and genome annotation files between assemblies. UCSC LiftOver is a pipeline that can be used to convert coordinate ranges between genome assemblies. It supports…

HomologSampler
Desktop

HomologSampler

A package to sample related sequences from Ensembl. HomologSampler provides…

A package to sample related sequences from Ensembl. HomologSampler provides capabilities to support sampling one-to-one orthologs from protein coding genes stored in an Ensembl MySQl database. It can…

orthoFind
Web

orthoFind

Searches for homologous and orthologous proteins at a genomics level. orthoFind…

Searches for homologous and orthologous proteins at a genomics level. orthoFind allows a quick search given one or more query sequences, and it can search either Swiss-Prot, a collection of reference…

Wheat Zapper
Web

Wheat Zapper

A fast and flexible on-line application to predict orthologous relationships…

A fast and flexible on-line application to predict orthologous relationships with the model species Oryza sativa, Brachypodium dystachyon, and Sorghum bicolor. Wheat Zapper was specifically designed…

OrthologID
Web

OrthologID

Allows for the rapid and accurate identification of gene orthology within a…

Allows for the rapid and accurate identification of gene orthology within a character-based phylogenetic framework.

PHOG
Web

PHOG PhyloFacts Orthology Group

Identifies orthologs based on phylogenetic analysis. PHOG provides a…

Identifies orthologs based on phylogenetic analysis. PHOG provides a combination of high recall and precision competitive with both InParanoid and OrthoMCL. It allows users to target different…

POPE
Desktop

POPE Phylogeny, Ortholog and Paralog Extractor

Provides an integrated platform for automatic ortholog identification. POPE…

Provides an integrated platform for automatic ortholog identification. POPE aids in phylogenetic data analysis using a large number of proteins. It includes routines to sort phylogenetic trees based…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.