From Bioinformatics.Org Wiki
- GenomePixelizer - Genome Visualization Tool: Detection of duplicating events in genomes, Displaying the Genetic Maps, Comparative genetics in general.
- PHASE - PHASE performs molecular phylogenetic inference using maximum likelihood and Bayesian (MCMC) techniques. Specific RNA substitution models are implemented to account for the correlated mutations of paired bases in RNA helices.
- T-REX - Horizontal gene transfer detection and validation, phylogenetic inference (PhyML, RAxML, NINJA, Neighbor Joining) and visualization.