From Bioinformatics.Org Wiki
Genomics is a field which existed before the completion of the sequences of genomes, but in the crudest of forms. For example the oft-re-referenced estimate of 100,000 genes in the human genome derived from a(n) (in)famous piece of "back of an envelope" genomics, guessing the weight of chromosomes and the density of the genes they bear. Genomics is any attempt to analyze or compare the entire genetic complement of a species or species (plural). It is, of course, possible to compare genomes by comparing more-or-less representative subsets of genes within genomes.
- MATLAB Bioinformatics Toolbox software provides access to genomic and proteomic data formats, analysis techniques, and specialized visualizations for genomic and proteomic sequence and microarray analysis.
- Clann - Clann: Software for investigating phylogenomic information using supertrees. This implements several methods of Supertree analysis (which are used as optimality criteria) and allows exhaustive and heuristic searches of tree-space to find the best supert
- ERGO - ERGO is an extensive microbial genome database including access to gene annotations, protein sequences, and networked metabolic/non-metabolic pathways. It also provides a number of tools for genome analysis and cellular pathway visualization.
- PyPhy - PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial genomes.