GenomePixelizer Download



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Check the latest version at: www.atgc.org

MatrixMining page (How to set up matrix for GenomePixelizer and PhyloGrapher)

Download Tcl/Tk toolkit from tcl.activestate.com



Reference: A. Kozik, E. Kochetkova, and R. Michelmore
GenomePixelizer-a visualization program for comparative genomics within and between species
Bioinformatics 2002 18: 335-336.

Download poster (PowerPoint presentation) from Plant, Animal & Microbe Genomes X Conference, San Diego, January 2002.

What is new (February 15 2002):
Completely re-wrote "Matrix Validator" and "Locus Zoomer" procedures, works much faster than in previous distribution.

A single-file binary executable for the Windows platform is available:
GenomePixelizer_February_15_2002.exe
the program can be distributed to Windows machines that do not have Tcl/Tk installed. To use it you need to download the full version of GenomePixelizer and Windows "exe" file, uncompress "GenoPixRelease_February_15_2002.tar.gz" using WinZip or other program, place "exe" file into "GenoPixRelease_February_15_2002" directory and run it by double-click. (binary "exe" file was generated by "FreeWrap" program http://freewrap.sourceforge.net)

What is new (January 07 2002):
1. Tcl/Tk and Perl scripts to parse results of Fasta or Blast searches in the "Scripts" directory. Tcl/Tk script to transform Phylip/ClustalW distance matrix file into "three column" matrix file in a "proper" GenomePixelizer format. Click here to find out how to use these scripts and generate matrix file using results of Fasta or Blast searches.
2. Revised Arabidopsis distance matrix file.

What is new (November 07): "Locus Zoomer" procedure; GenomePixelizer allows to zoom in semi-automatic mode into regions of interest and generate sub-projects by extracting data from whole dataset. Click here to view an example.
"Gene Painter" procedure; GenomePixelizer allows to paint different set of genes in different colors in batch mode dynamically, without re-running the project.
"Matrix Color Tuner" procedure; GenomePixelizer allows to assign color for "similarity/identity" lines based on distance matrix file data dynamically, without changing the source of input file.

What is new (August 21): "Horizontal size of gene" is variable, You may run GenomePixelizer in standard (no difference from previous version) or extended mode. (see last line of GenPix_RunSetup file). An optional "Matrix Validator" procedure, which allows you to check the proper setup of a matrix file.

What is new (July 27): "Canvas Editor", you may add text and graphical labels to images generated by GenomePixelizer or the Alignment Viewer; minor bug fixes, almost all parameters are variables now. (see GenPix_RunSetup file).

What is new (July 01): "Save as PostScript" functionality, minor bug fixes, improved color scheme, chromosome color is variable, minor changes in documentation.


Old version (tar.gz), February 15 2002.
Old version (tar.bz2), February 15 2002.
Old version, January 07 2002
Old version, November 07 2001
Old version, August 21 2001
Old version, July 27 2001
Old version, July 01 2001
Old version, June 25 2001
Old version, June 20 2001
Old version, June 15 2001
Old version, June 11 2001
Old version, May 31 2001




Description
Screenshots
Examples
Manual
Download
Feedback
Authors


email: Alexander Kozik

Last modified, July 03 2002