Several of our recent software projects are hosted here.
GenGIS – Geospatial Analysis of Environmental Genomic Data
Remarkably, some of my postdoc software is still alive and kicking, although it probably has more anthropological than scientific value:
EEEP – Efficient Evaluation of Edit Paths to infer lateral genetic transfer events from phylogenetic tree comparisons: biologically sound but sluggish, superseded by the algorithmic magic of rSPR.
EvolSimulator – simulation of gene, protein, and genome evolution: A super-fun tool to simulate lateral gene transfer under different hypotheses of biased gene transfer.
The data from the 2005 PNAS paper “Highways of gene sharing in prokaryotes” can be found here.