Scientific programs

ExP Heatmap (by Edvard Ehler and Jan Paces): Extended Cross-Population Heatmap, visualization of highly dimentional datasets of pairwise values. Designed to display results (significance, p-values) for cross-population selection tests for 1000 Genomes, phase 3 sample-set, but can be tweaked to display the results for arbitrary number of groups/populations.
LOHIRIA (by Jan Paces & Jakub Galgonek): Localization of High Identity Regions In Alignment. Program designed for helping with alergenic assesment (rules by WHO) or horizontal gene transfer (guidance by EFSA). (by Jan Paces): This program is in perl. It is designed for drawing pictures of gc profiles of long nucleotide sequences, e.g. whole chromosomes. This version needs to have installed perl (>5.0) with module. Everything you need you can find at CPAN.
DicodonUsage (by Jan Paces): This set of perl scripts visualize dicodon bios in procaryotic genomes. It consist from, which counts dicodons in given training set and two scripts and, which draw dicodon preferences for six reading frames.
right handphyloMOD (by Simone Scalabrin): Perl script to compare orthologous sequences and extract putative regulatory regions. It is based on modular structure of regulatory regions and phylogenetic footprinting of orthologous sequences.

Jan Paces
Last modified: Thu Apr 7 15:20:46 CEST 2005
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