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 and complete genomes.
Source text:
(Nielsen et al., 2010) Visualizing genomes: techniques and challenges. Nat Methods.
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…
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…
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…
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…
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…
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…
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.
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…
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…
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…
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…
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…
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…
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,…
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…
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.
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…
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…
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…
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.
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…
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…
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.
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…
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…
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.
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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