TopiaryExplorer 1.0 – Interactive Phylogenetic Tree Viewing software

TopiaryExplorer 1.0

:: DESCRIPTION

TopiaryExplorer supports visualization of very large trees (it has been tested on trees with > 100,000 tips) while providing convenient interfaces for decorating the tree with taxonomic information, automatically coloring branches based on data about environments where they are observed, selecting subtrees for independent analysis, interactive expanding and collapsing of clades, and many other features.

::DEVELOPER

Knight Lab

:: SCREENSHOTS

TopiaryExplorer

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Java

:: DOWNLOAD

 TopiaryExplorer

:: MORE INFORMATION

Citation

Pirrung, M., R. Kennedy, J. G. Caporaso, J. Stombaugh, D. Wendel, and R. Knight. 2011.
TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata.
Bioinformatics 27, no. 21 (October 21): 3067–3069. http://dx.doi.org/10.1093/bioinformatics/btr517.

VisIt 2.9 – Visualization and Analysis tool for Viewing Scientific Data

VisIt 2.9

:: DESCRIPTION

VisIt is a free interactive parallel visualization and graphical analysis tool for viewing scientific data on Unix and PC platforms. Users can quickly generate visualizations from their data, animate them through time, manipulate them, and save the resulting images for presentations. VisIt contains a rich set of visualization features so that you can view your data in a variety of ways. It can be used to visualize scalar and vector fields defined on two- and three-dimensional (2D and 3D) structured and unstructured meshes. VisIt was designed to handle very large data set sizes in the terascale range and yet can also handle small data sets in the kilobyte range.

::DEVELOPER

the Department of Energy (DOE) Advanced Simulation and Computing Initiative (ASCI)

:: SCREENSHOTS

VisIt

:: REQUIREMENTS

  • MacOsX /Windows/Linux

:: DOWNLOAD

 VisIt

:: MORE INFORMATION

Diurnal 2.0 – Mining and Viewing Diurnal and Circadian Microarray data for Arabidopsis thaliana, poplar, and rice

Diurnal 2.0

:: DESCRIPTION

Diurnal is a web-based tool for accessing the diurnal and circadian genome-wide expression results of genes from several array experiments conducted on common model plants. The expression patterns of particular loci or array probes can be looked up under a variety of different conditions. For each condition, every expression pattern has been modeled using a periodic pattern, which has then been used to estimate the phase of peak expression.

::DEVELOPER

Mockler Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis.
Mockler TC, Michael TP, Priest HD, Shen R, Sullivan CM, Givan SA, McEntee C, Kay SA, Chory J.
Cold Spring Harb Symp Quant Biol. 2007;72:353-63. doi: 10.1101/sqb.2007.72.006.

TraceView 2.01 – Java Applet for viewing Sequence Traces

TraceView 2.01

:: DESCRIPTION

TraceView is a set of trace viewing tools with each component filling a different software niche.

::DEVELOPER

Jeremy Parsons

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 TraceView

:: MORE INFORMATION

Citation

Genome Res. 1999 Mar;9(3):277-81.
DNA sequence chromatogram browsing using JAVA and CORBA.
Parsons JD, Buehler E, Hillier L.

SStructView 1.2.2 – RNA Secondary Structure Viewing Java Applet

SStructView 1.2.2

:: DESCRIPTION

SStructView is a Java applet for viewing RNA secondary structures and linking to multiple computational backends. SStructView supports colored bases, standard mouse selection mechanisms (drag to select a range, control-click to select individuals), arbitrary set-based data types to allow you to create your own groups, and other improvements.RNA biologists who want an extendible java application for viewing RNA secondary structure.

::DEVELOPER

Ramon M. Felciano, Richard Chen and Russ Altman, Helix Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

SStructView

:: MORE INFORMATION

Citation

R. M. Felciano, R. O. Chen, & R. B. Altman.
RNA Secondary Structure as a Reusable Interface to Biological Information Resources.
Gene 190 (1997) GC59-70

GSCANDB 1.0 – Portable System for Managing and Viewing Genome Scan Data

GSCANDB 1.0

:: DESCRIPTION

GSCANDB is a portable system for managing and viewing genome scan data.

::DEVELOPER

Richard Mott

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MySQL
  • Perl-CGI
  • Apache
  • JAVA
  • ANT

:: DOWNLOAD

 GSCANDB

:: MORE INFORMATION

Citation

Taylor M, Valdar W, Kumar A, Flint J, Mott R.
Management, presentation and interpretation of genome scans using GSCANDB.
Bioinformatics. 2007 Jun 15;23(12):1545-9. Epub 2007 Mar 30.

GelScape 20030728 – Web-based Gel Viewing and Annotation System

GelScape 20030728

:: DESCRIPTION

GelScape offers a freely available, platform-independent approach to analyzing standard 1D and 2D protein gels.  GelScape uses advanced concepts in “network computing” enabling one to upload, download, save, print, view, annotate, edit, label, compare and spot mark just about any gel image.  GelScape also allows one to calculate spot intensity, prepare HTML image maps and archive annotated gels to a public database (GelBank) – all using an easy-to-use, intuitive browser interface.

::DEVELOPER

Wishart Pharmaceutical Research Group

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 GelScape

:: MORE INFORMATION

Citation

Young N, Chang Z, Wishart DS.
GelScape: a web-based server for interactively annotating, manipulating, comparing and archiving 1D and 2D gel images.
Bioinformatics. 2004 Apr 12;20(6):976-8.