| AMAP | Protein multiple alignment based on alignment metric accuracy |
| GENEMAPPER | Reference based gene annotation |
| KBROWSER | Browser for multiple genomes and their alignments |
| MAVID | Multiple alignment of large genomic sequences |
| MERCATOR | Homlogy mapping |
| MJOIN | Neighbor joining with phylogenetic diversity estimates |
| PARALIGN | Alignment polytope construction |
| SHADOWER | Comparisons of multiple closely related species |
| SLAM | Pairwise simultaneous alignment and gene finding |
| SLIM | Minimum network design for optimizing the search space for pair HMMs |
| VISTA | Visualization tool for global alignments |
