Table 6 Visualization tools for comparative genomics

ACT [255]

A tool for displaying pairwise comparisons between two or more DNA sequences

http://www.sanger.ac.uk/Software/ACT/

Standalone

cBio [109]

An open-access resource for interactive exploration of multidimensional cancer genomics datasets

http://cbioportal.org

Web-based

Cinteny [256]

Detection of syntenic regions across multiple genomes and measuring the extent of genome rearrangement using reversal distance as a measure

http://cinteny.cchmc.org/

Web-based

Circos [107]

A software package for visualizing data and information. It visualizes data in a circular layout

http://mkweb.bcgsc.ca/circos

Standalone

CMap [257]

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

http://gmod.org/wiki/CMap

Standalone

CoGe SynMap [258]

Generates a syntenic dot-plot between two organisms and identifies syntenic regions

https://genomevolution.org/coge/SynMap.pl

Web-based

Combo [234]

Dot-plot and linked-track views. Integration of annotation in both views

http://www.broadinstitute.org/annotation/argo/

Standalone

DHPC [259]

Visualization of large-scale genome sequences by mapping sequences into a 2D using the space-filling function of Hilbert-Peano mapping

http://www.hpcurve.com

Standalone

DNAPlotter [260]

A Java application for generating circular and linear representations of genomes. Makes use of the Artemis libraries

http://www.sanger.ac.uk/resources/software/dnaplotter/

Standalone

FilooT [261]

A visualization tool for exploring genomic data

No URL

Standalone

GBrowsesyn [262]

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

http://gmod.org/wiki/GBrowse_syn

Standalone

GenomeComp [263]

A tool for summarizing, parsing and visualizing the genome-wide sequence comparison results derived from voluminous BLAST textual output

http://www.mgc.ac.cn/GenomeComp/

Standalone

GenomeMatcher [264]

A dot-plot-based viewer for DNA sequence comparison

http://tinyurl.com/genomematcher/

Web-based

GenPlay Multi-Genome [265]

A tool to compare and analyze multiple human genomes in a graphical interface

http://genplay.einstein.yu.edu

Standalone

ggbio [266]

R library to visualize particular genomic regions and genome-wide overviews

http://www.bioconductor.org/packages/2.11/bioc/html/ggbio.html

Standalone

Gramene [267, 268]

A comparative genome mapping database for grasses and a community resource for Oryza sativa

http://ensembl.gramene.org/genome_browser/index.html

Web-based

HilbertVis [269]

Functions to visualize long vectors of integer data by means of Hilbert curves

http://www.ebi.ac.uk/huber-srv/hilbert/

Standalone

In-GAVsv [270]

Integrative genome analysis pipeline (inGAP), which uses a Bayesian principle to detect SNPs and small insertion/deletions (indels)

http://ingap.sourceforge.net/

Standalone

Meander [271]

Hilbert plots to visually discover and explore structural variations in a genome based on read-depth and pair-end information

https://sites.google.com/site/meanderviz/

Standalone

MEDEA [272]

Genomic feature densities and genome alignments of circular genomes. Comparative genomic visualization with Adobe Flash

http://www.broadinstitute.org/annotation/medea/

Web-based

MizBee [273]

A multiscale synteny browser for exploring conservation relationships in comparative genomics data. Using side-by-side linked views, it enables efficient data browsing across a range of scales, from the genome to the gene

http://www.cs.utah.edu/~miriah/mizbee

Web-based

MuSiC [274]

Identifying mutational significance in cancer genomes

http://gmt.genome.wustl.edu

Standalone

ngs.plot [275]

Quick mining and visualization of NGS data by integrating genomic databases

https://github.com/shenlab-sinai/ngsplot

Standalone

PhIGs [276]

Ideogram-style interactive display of orthologs across >75 genomes

http://phigs.org

Web-based

PSAT [277]

A web tool to compare genomic neighborhoods of multiple prokaryotic genomes

http://www.nwrce.org/psat

Web-based

Seevolution [278]

Interactive 3D environment that enables visualization of diverse genome evolution processes

http://seevolution.org

Standalone

Sybil [279]

Comparative genome data, particularly protein and gene clustered data

http://sybil.sourceforge.net/

Web-based

SynView [238]

A GBrowse-compatible approach to visualizing comparative genome data

http://gmod.org/wiki/SynView

Standalone

TREAT [280]

A bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data

http://ndc.mayo.edu/mayo/research/biostat/stand-alone-packages.cfm

Standalone

UCSC Genome Browser [281]

Conservation tracks within the popular UCSC genome browser

http://genome.ucsc.edu/cgi-bin/hgGateway/

Web-based

Vanno [282]

A visualization-aided variant annotation tool

http://cgts.cgu.edu.tw/vanno

Web-based

Variant View [283]

Features an information-dense visual encoding that provides maximal information at the overview level, in contrast to the extensive navigation required by currently prevalent genome browsers

http://www.cs.ubc.ca/labs/imager/tr/2013/VariantView/

Web-based

VISTA [108]

A comprehensive suite of programs and databases for comparative analysis of genomic sequences

http://genome.lbl.gov/vista/index.shtml

Web-based

VSV, VISTA-Dot [284, 285]

Three-scale viewer for synteny and dynamic, interactive dot plots for whole-genome DNA alignments

http://genome.jgi-psf.org/synteny/

Web-based