Visualization Tools

VisualizationTools Used

Visualization

Ensemblproduces genome databases for vertebrates and other eukaryotic species

JalViewJalView is a free program for multiple sequence alignment editing, visualization and analysis.

Use it to view and edit sequence alignments, analyze them with phylogenetic trees and principal components analysis (PCA) plotNExs and explore molecular structures and

annotation.

G-CompassComparative genome browser.

G-Compass

– Visualizes evolutionarily conserved genomic regions between human and other 12 vertebrates

– 12 Vertebrates Include:• Chicken, Chimpanzee, Cow, Dog, Horse, Macaque, Medaka, Mouse, Rat, Tetraodon,

Opossum, & Zebrafish

JBrowseSpeedy genome browser with a responsive and dynamic Ajax interface for visualization of

genome data

JBrowse

TabletA lightweight, high-performance graphical viewer for ngs assemblies and alignments

Tablet

Tablet showing Illumina Solexa reads against an Arabidopsis thaliana cDNA reference sequence

(additional screenshots can be seen online at http://bioinf.scri.ac.uk/tablet/screenshots.shtml).

Milne I et al. Bioinformatics 2010;26:401-402

© The Author(s) 2009. Published by Oxford University Press.

Work Cited“Jbrowse.” SEQwiki, N.P., 6 Feb. 2013. Web. 11 Aug. 2014.

<http://seqanswers.com/wiki/JBrowse>.Kawahara, Y., R. Sukate, A. Matsuya, K. Murakami, Y. Sato, H. Zhang, T. Gojobori, To. Itoh, and T.

Imanishi. “G-compass: a we-based comparative genome browse between human and other vertebrate genomes.” Bioinformatics 25.24 (2009): 3321-3322. Print.

Lee E et al. Web Apollo: a web-based genomic annotation editing platform. Genome Biology. (2013) DOI;1Q.1186/gb-2013-14-8-r93 PMID;24000942

Skinner ME, Homes IH. Setting up the Jbrowse genome browser. Curr Protoc Bioinformatics. (2010).

Skinner, ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH. Jbrowse: A next-generation genome browser.

Genome Res. (2009).