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, heuristic algorithms based on…
Web app
ORtholog sCANner ORtholog sCANner

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…

Desktop app
G T A T C G C T A De-Novo Genome… De-Novo Genome Analysis Pipeline

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…

Web app
WORM Human OrthoLogy… WORM Human OrthoLogy Explorer

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,…

Desktop app
FamFetch FamFetch

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…

Desktop app
Hierarchical… Hierarchical Orthology Inference

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.…

Desktop app
Duplication, Loss,… Duplication, Loss, Rate and Sequence Orthology

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…

Desktop app
HOmology Mapper for… HOmology Mapper for Enrichment and Comparative…

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…

Web app
Fast Approximate Tree… Fast Approximate Tree Classification

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…

Desktop app
GeneSeqToFamily GeneSeqToFamily

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…

Desktop app
HomologSampler HomologSampler

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…

Desktop app
Bi-Directional BLAST Bi-Directional BLAST

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…

Desktop app
Levels of Orthology… Levels of Orthology From Trees

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…

Desktop app
OGCleaner OGCleaner

OGCleaner

A python software package for filtering putative homology clusters of amino…

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

Web app
orthoFind orthoFind

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…

Web app
Wheat Zapper Wheat Zapper

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…

Desktop app
OrthoFinder OrthoFinder

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 %…

Desktop app
COmpare genomes with… COmpare genomes with SEgmental duplications and…

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…

Desktop app
MSOAR MSOAR

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…

Web app
OrthoVenn OrthoVenn

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…

Desktop app
DOmain based… DOmain based Detection of Orthologs

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…

Web app
Orthologous Mammalian… Orthologous Mammalian Markers

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…

Web app
morFeus morFeus

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…

Desktop app
OrthoClust OrthoClust

OrthoClust

For simultaneously clustering data across multiple species.

For simultaneously clustering data across multiple species.

Desktop app
COCO-CL COCO-CL

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…

Desktop app
Web app
SPOCS SPOCS

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.

Desktop app
Proteinortho Proteinortho

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.

Web app
OrthologID OrthologID

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.

Desktop app
OrthoInspector OrthoInspector

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…

Desktop app
orthAgogue orthAgogue

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.

Web app
Orthologous MAtrix Orthologous MAtrix

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,…

Web app
PhyloFacts Orthology… Deprecated PhyloFacts Orthology Group

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…

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