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).
draw_chromosome_gc.pl(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 GD.pm module. Everything you need you can find at CPAN.
All GC-profiles of eukaryotic genenomes are on this site
DicodonUsage(by Jan Paces): This set of perl scripts visualize dicodon bios
in procaryotic genomes. It consist from count_dicodons.pl, which counts dicodons in given training
set and two scripts dicodons.pl and dicodons_seq.pl, which draw dicodon preferences for
six reading frames.
example 1 (Rhodobacter_capsulatusdicodon.pl - large scale)
example 2 (Rhodobacter_capsulatusdicodon_seq.pl - small scale)
phyloMOD(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.