The recent availability of a large number of completely sequenced and assembled genomes has stimulated active research in the field of comparative genomics. This includes the development of algorithms and tools for pairwise and multiple alignment of very long genomic intervals…
Web app
University of… University of California Santa Cruz Genome Browser

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…

Desktop app
Web app
Artemis Comparison… Artemis Comparison Tool

ACT Artemis Comparison Tool

A free tool for displaying pairwise comparisons between two or more DNA…

A free tool for displaying pairwise comparisons between two or more DNA sequences. ACT can be used to identify and analyse regions of similarity and difference between genomes and to explore…

Desktop app
Circos Circos

Circos

It visualizes data in a circular layout - this makes Circos ideal for exploring…

It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.

Desktop app
GenPlay GenPlay

GenPlay

An analyzer and browser for high-throughput data. GenPlay recognizes a wide…

An analyzer and browser for high-throughput data. GenPlay recognizes a wide variety of common genomic data formats from microarray- or sequencing-based platforms and offers a library of operations…

Desktop app
Mauve Mauve

Mauve

A system for constructing multiple genome alignments in the presence of…

A system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignments provide a basis for research…

Desktop app
Easyfig Easyfig

Easyfig

A Python application for creating linear comparison figures of multiple genomic…

A Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface. BLAST comparisons between multiple genomic regions, ranging from…

Web app
Sybil Sybil

Sybil

Provides a feature-rich set of comparative genomics tools for inspection of…

Provides a feature-rich set of comparative genomics tools for inspection of multiple genome structures, mining of orthologous gene families and identification of potential vaccine candidates. The…

Desktop app
GenomeMatcher GenomeMatcher

GenomeMatcher

A standalone to visualize similarities between two DNA sequences. GenomeMatcher…

A standalone to visualize similarities between two DNA sequences. GenomeMatcher executes BLAST and MUMmer, and the detected similarities are displayed in two-dimensional and parallel views with…

Desktop app
BLAST Ring Image… BLAST Ring Image Generator

BRIG BLAST Ring Image Generator

A cross-platform (Windows/Mac/Unix) application that can display circular…

A cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.

Desktop app
Synteny Browser Synteny Browser

SynBrowse Synteny Browser

A generic sequence comparison tool for visualizing genome alignments both…

A generic sequence comparison tool for visualizing genome alignments both within and between species.

Desktop app
SynView SynView

SynView

A GBrowse-compatible approach to visualizing comparative genome data.

A GBrowse-compatible approach to visualizing comparative genome data.

Desktop app
Generic Synteny… Generic Synteny Browser

GBrowse_syn Generic Synteny Browser

A GBrowse-based synteny browser designed to display multiple genomes, with a…

A GBrowse-based synteny browser designed to display multiple genomes, with a central reference species compared to two or more additional species.

Desktop app
CMap CMap

CMap

A browser-based tool for the visual comparison of various maps (sequence,…

A browser-based tool for the visual comparison of various maps (sequence, genetic, etc.) from any number of species.

Web app
Genome Synteny Viewer Genome Synteny Viewer

GSV Genome Synteny Viewer

An option for biologists to analyze genome synteny by uploading their own data…

An option for biologists to analyze genome synteny by uploading their own data set to a web-based comparative genome browser. Allows users to upload two data files for synteny visualization, the…

Desktop app
GenomeRing GenomeRing

GenomeRing

Creates an interactive overview visualization of the multiple genome alignment…

Creates an interactive overview visualization of the multiple genome alignment in a circular layout. GenomeRing is a highly interactive tool for multiple alignment visualization based on SuperGenome…

Desktop app
Comparative Genome… Comparative Genome Analysis Tool

CGAT Comparative Genome Analysis Tool

A Comparative Genome Analysis Tool that was developed for detailed comparison…

A Comparative Genome Analysis Tool that was developed for detailed comparison of closely related bacterial-sized genomes.

Desktop app
MizBee MizBee

MizBee

A multiscale synteny browser for exploring conservation relationships in…

A multiscale synteny browser for exploring conservation relationships in comparative genomics data.

Web app
Multi-Image Genome Multi-Image Genome

MIG Multi-Image Genome

A web-based application for visualizing, querying and filtering many thousands…

A web-based application for visualizing, querying and filtering many thousands of genome browser regions as well as for exporting the data in a variety of formats. MIG allows the user to generate…

Web app
G-compass G-compass

G-compass

It visualizes evolutionarily conserved genomic regions between human and other…

It visualizes evolutionarily conserved genomic regions between human and other 12 vertebrates based on original genome alignments pursuing higher coverage.

Web app
Gobe Gobe

Gobe

A web-based tool for viewing comparative genomic data. Gobe supports viewing…

A web-based tool for viewing comparative genomic data. Gobe supports viewing multiple genomic regions simultaneously. Its simple text format and flash-based rendering make it an interactive,…

Desktop app
PipMaker/MultiPipMaker PipMaker/MultiPipMaker

PipMaker/MultiPipMaker

Computes alignments of similar regions in two DNA sequences. Moreover,…

Computes alignments of similar regions in two DNA sequences. Moreover, MultiPipMaker can be requested to compute a true multiple alignment of the input sequences and return a nucleotide-level view of…

Web app
VISTA Browser VISTA Browser

VISTA Browser

A Java applet, very efficient for interactively visualizing results of…

A Java applet, very efficient for interactively visualizing results of comparative sequence analysis in the VISTA format on the scale of whole chromosomes along with annotations. The user may select…

Desktop app
JContextExplorer JContextExplorer

JContextExplorer

Organizes genomic contexts into branching diagrams. To facilitate genomic…

Organizes genomic contexts into branching diagrams. To facilitate genomic context analysis, it implements Graphical User Interface (GUI) features, such as text search filtering, point-and-click…

Web app
Desktop app
Millstone Millstone

Millstone

Supports an iterative process of multiplex mutation analysis and genome…

Supports an iterative process of multiplex mutation analysis and genome engineering. Millstone automates read alignment and variant calling using a hybrid reference-based and de novo assembly…

Web app
Multi Genome Viewer Multi Genome Viewer

GECKO-MGV Multi Genome Viewer

A web app to display, browse and analyse the results of genome comparison…

A web app to display, browse and analyse the results of genome comparison produced by GECKO and GECKO-CSB. This tool is composed of several independent modules that execute specific tasks for the…

Desktop app
CrusView CrusView

CrusView

A Java-based bioinformatic application utilizing Standard Widget Toolkit/Swing…

A Java-based bioinformatic application utilizing Standard Widget Toolkit/Swing graphics libraries and a SQLite database for performing visualized analyses of comparative genomics data in Brassicaceae…

Desktop app
genoPlotR genoPlotR

genoPlotR

Generates reproducible maps of genes and genomes that can be used to generate…

Generates reproducible maps of genes and genomes that can be used to generate publication-ready figures, starting from a wide range of formats. Since all the instructions for drawing the figures are…

Desktop app
Coulson Plot Generator Coulson Plot Generator

CPG Coulson Plot Generator

A graphical representation tool to display and compare genomics data. CPG…

A graphical representation tool to display and compare genomics data. CPG allows users to rapidly convert spreadsheet data to a graphical matrix pie chart format. Pie charts are arranged by…

Desktop app
YouGenMap YouGenMap

YouGenMap

A genetic map viewer that allows users to upload, display, download, update,…

A genetic map viewer that allows users to upload, display, download, update, search, share, and compare sets of mapping and marker annotation data. YouGenMap allows users to visualize multiple map…

Web app
INSYGHT INSYGHT

INSYGHT

A comparative genomic visualization tool that combines three complementary…

A comparative genomic visualization tool that combines three complementary displays: (i) a table for thoroughly browsing amongst homologues, (ii) a comparator of orthologue functional annotations and…

Web app
Genome Presence… Genome Presence Absence Compiler

GPAC Genome Presence Absence Compiler

A tool to facilitate the parallel analysis of thousands of genomic loci for…

A tool to facilitate the parallel analysis of thousands of genomic loci for cross-species presence/absence patterns based on multiway genome alignments. This genome presence/absence compiler uses…

Desktop app
Sockeye Sockeye

Sockeye

A Java application designed to assemble, view and work with genomic information…

A Java application designed to assemble, view and work with genomic information in a 3D environment. Sockeye has been developed with a focus on displaying potential gene regulatory regions and for…

Web app
Cinteny Cinteny

Cinteny

Compares multiple genomes and performs sensitivity analysis for synteny block…

Compares multiple genomes and performs sensitivity analysis for synteny block detection and for the subsequent computation of reversal distances. Cinteny can also be used to interactively browse…

Desktop app
Trebol Deprecated Trebol

Trebol

A multi-platform software for comparative genome analyses with functionalities…

A multi-platform software for comparative genome analyses with functionalities such as sequence retrieving, generation of sequence comparisons, visualization, edition and rendering of high quality…

Web app
Alvira Deprecated Alvira

Alvira

A general purpose multiple sequence alignment viewer with a special emphasis on…

A general purpose multiple sequence alignment viewer with a special emphasis on the comparative analysis of viral genomes. Alvira has been devised specifically to address the problem of the…

Desktop app
MEDEA Deprecated MEDEA

MEDEA

A visualization suite that consists of the Circular Genome Viewer, Stack Map,…

A visualization suite that consists of the Circular Genome Viewer, Stack Map, ChromoMap, Dot Plot, and Viral Viewer. MEDEA is a suite of Adobe Flash based comparative genomic : the MEDEA Circular…

Advertisements
Join Omic Community

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