GenomePixelizer Download


Download current version (tar.gz), October 01 2003.

Arabidopsis Genome dataset corresponding to recent annotation (TIGR Release Version 4.0, May 2003)

BLAST parser (This parser creates Matrix file for GenomePixelizer automatically using BLAST run results)

GenBank parser:

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

Download Tcl/Tk toolkit from

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.

Download poster (PowerPoint presentation) from Plant, Animal & Microbe Genomes XI Conference, San Diego, January 2003.

Download poster (PowerPoint presentation) from Plant, Animal & Microbe Genomes XII Conference, San Diego, January 2004.

What is new (October 01 2003):
Function "Locus Zoomer" did not work properly when both loci belong to the same chromosome. It was fixed in the current version.

A single-file binary executable for the Windows platform is available:
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_October_01_2003.tar.gz" using WinZip or other program, place "exe" file into "GenoPixRelease_October_01_2003" directory and run it by double-click. (binary "exe" file was generated by "FreeWrap" program

What is new (June 24 2003):
If user provides "Annotation File" (see "What is new" - May 05 2003) then canvas is searchable by keywords from annotation. In the case of successful search all genes containing particular keyword (kinase, for example) will be painted into color defined in "Canvas Editor" window for graphical labels. Selected genes can be painted back to original color scheme by clicking on "Update (Color Reset)" button on "Canvas Manipulator" window.

What is new (May 05 2003):
Mouse click event displays gene annotation in the "Annotation Window" if the corresponding tab-delimited file with gene description is defined in the Run_Setup file (option #19). For details check the example RunSetup_Arab_chr_5_vs_4.txt

What is new (April 03 2003):
Updated Arabidopsis genome (TIGR version of January 2003). New "Canvas Manipulator" procedure helps to finish canvas layout. Re-written similarity line-plot procedure. Improved color scheme. "Scripts" directory contains BLAST parser to generate Matrix file automatically based on BLAST results.

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

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 2001): "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 2001): "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 2001): "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 2001): "Save as PostScript" functionality, minor bug fixes, improved color scheme, chromosome color is variable, minor changes in documentation.

previous version, June 24 2003
previous version, May 05 2003
previous version, April 03 2003
previous version, February 15 2002


email: Alexander Kozik

Last modified, January 26 2004