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Comparative genome visualization software tools | Comparative genomics

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…
GenPlay
Desktop

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…

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…

Genomicus
Web

Genomicus

A visualization tool allowing comparative genomics in four different phyla…

A visualization tool allowing comparative genomics in four different phyla (Vertebrate, Fungi, Metazoan and Plants). Genomicus provides access to genomic information from extant species, as well as…

ACT
Desktop
Web

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…

Circos
Desktop
Web

Circos

Displays large volumes of genomic rearrangement data. Circos is a visualization…

Displays large volumes of genomic rearrangement data. Circos is a visualization tool that applies a circular ideogram layout to display relationships between genomic intervals. The software provides…

Sybil
Web

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…

BRIG
Desktop

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.

The Genetic…
Web
Desktop

The Genetic Map Comparator

Compares genetic maps according to their key statistics and the relative…

Compares genetic maps according to their key statistics and the relative positions of common markers. The Genetic Map Comparator allows users to compare maps via standard statistics (number of…

Mauve
Desktop

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…

GenomeMatcher
Desktop

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…

Easyfig
Desktop

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…

GPAC
Web

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…

INSYGHT
Web

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…

Gobe
Web

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,…

BLASTGrabber
Desktop

BLASTGrabber

Explores high-throughput BLAST output generated from large scale database…

Explores high-throughput BLAST output generated from large scale database searches. BLASTGrabber aims to facilitates visualization, analysis and selection of data. The software allows users to apply…

CMap
Desktop

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.

GenomeRing
Desktop

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…

MIG
Web

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…

CrusView
Desktop

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…

CGAT
Desktop

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.

CCT
Desktop

CCT CGView Comparison Tool

Permits to build or modify complex maps potentially involving thousands of…

Permits to build or modify complex maps potentially involving thousands of sequences. CCT is suited to the analysis of large collections of complete or partial genomes generated through…

Millstone
Web
Desktop

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…

GBrowse_syn
Desktop

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.

genoPlotR
Desktop

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…

BlastGraph
Desktop

BlastGraph

Generates and visualizes clusters as a graph with accompanying statistics,…

Generates and visualizes clusters as a graph with accompanying statistics, evaluation metrics and associated background information. BlastGraph is a user-friendly application for comparative genomics…

G-compass
Web

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.

Sockeye
Desktop

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…

GECKO-MGV
Web

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…

YouGenMap
Desktop

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…

PipMaker/MultiP…
Desktop

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…

JContextExplore…
Desktop

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…

VISTA Browser
Web

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…

CPG
Desktop

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…

WebACT
Web

WebACT

Allows to compare genomic sequences. WebACT is an online resource providing…

Allows to compare genomic sequences. WebACT is an online resource providing BLAST comparison and sequence files in appropriate formats for ACT. It permits the generation of comparisons based on…

3D Genome Tuner
Desktop

3D Genome Tuner

Enables comparing circular genomes in a 3D space. 3D Genome Tuner is a hybrid…

Enables comparing circular genomes in a 3D space. 3D Genome Tuner is a hybrid of circular map and comparative map tools. Its capability of viewing comparisons between multiple circular maps in a 3D…

Trebol
Desktop

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…

Cinteny
Web

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…

Aquerium
Web

Aquerium Architecture Querying Podium

Visualizes genomic presence and absence of biomolecules with a focus on protein…

Visualizes genomic presence and absence of biomolecules with a focus on protein domain architectures. Aquerium offers advanced domain organization querying against the database of pre-computed…

CGAP
Web

CGAP Chloroplast genome analysis platform

Simplifies the analysis of complete chloroplast genomes. CGAP contains genome…

Simplifies the analysis of complete chloroplast genomes. CGAP contains genome collection, visualization, content comparison, phylogeny analysis and annotation functions. It implements feature content…

CMap3D
Desktop

CMap3D

Compares and visualizes multiple genetic maps. CMap3D allows users to add…

Compares and visualizes multiple genetic maps. CMap3D allows users to add genetic maps to the three-dimensional (3D) viewing space to detect correspondence between them and interact with the viewing…

Alvira
Web

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…

BOV
Web
Desktop

BOV BLAST Output Visualization

Allows users to interactively visualize the matching regions of query and…

Allows users to interactively visualize the matching regions of query and database hit sequences, thereby allowing the user to quickly and easily dissect complex matching patterns. BOV extracts the…

MEDEA
Desktop

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…

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