TreeBuilder3D 1.0 – Interactive Viewer for Gene Expression Data

TreeBuilder3D 1.0

:: DESCRIPTION

TreeBuilder3D is an interactive viewer that allows organization of SAGE and other types of gene expression data such as microarrays into hierarchical dendrograms, or phenetic networks (the term ‘phenetic’ used as the analysis relies on principals, used in phylogenetic analysis by system biology). Might be used as a visual aid when analyzing differences in expression profiles of SAGE libraries, serves as an alternative to Venn diagrams.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Mac / Linux
Java
Java3D

:: DOWNLOAD

TreeBuilder3D

:: MORE INFORMATION

Citation

Ruzanov P, Jones SJ.
An interactive tool for visualization of relationships between gene expression profiles.
BMC Bioinformatics. 2006 Apr 6;7:193.

inSite – Interactive Viewer for Comparing Patterns of Binding Sites across multiple Genomics Regions

inSite

:: DESCRIPTION

inSite (interactive site viewer) is a tool for interactively visualizing binding sites along multiple genomic regions. Different types of transcription factors are encoded with color with a user-defined, interactive color legend.

::DEVELOPER

Miriah Meyer & DePace Lab

:: SCREENSHOTS

:: REQUIREMENTS

Linux/ Windows/ MacOsX

:: DOWNLOAD

inSite

:: MORE INFORMATION

Gmaj 20081103 – Interactive Viewer for Multiple Sequence Alignments

Gmaj 20081103

:: DESCRIPTION

Gmaj is a tool designed for viewing and manipulating Generalized Multiple Alignments (GMAs) produced by sequence-symmetric alignment programs such as TBA (though it can also be used with MAF format alignments from other sources). It can display interactive graphical and text representations of the alignments, diagrams showing the locations of exons and repeats, and other annotations — all with the user’s choice of reference sequence.

::DEVELOPER

Miller Lab at Penn State University Center for Comparative Genomics and Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java

:: DOWNLOAD

Gmaj

:: MORE INFORMATION