Bioinformatics software
I wrote a few bioinformatics tools while I was at UQAM and some of them are acually usable so instead of letting them sit on my hard-drive I put them here for you to enjoy.
Pipviewer
Pipviewer is a visualizer for multiple alignments of genomic sequences. It highlights conserved regions and allows basic anotations. Its main goal is to find conserved probes for the construction of gene order data sets. Selected regions marked as 'probes' can be exported to fasta format. It can also retrieve gene annotations form the NBCI and display this information along the alignment. Pipviewer is not an aligner. You must compute the alignment with another tool like Clustal or Multi PIP Maker.
Vhybridize
This package contains Virtual Hybridization command line tools. Virtual Hybridization uses sets of short probes to generate datasets for comparative genomics: given a DNA sequence and a set of probes, the typical output will give a sequence of oriented probe hits along the DNA sequence. Other tools are supplied to allow simple manipulations such as format conversion and extraction of permutations.
Typically, you'll select a probe set with pipviewer and use it to produce gene order datasets on multiple genomes with vhybridize.
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Here are the latest versions: