Table 5.
A suite of programs to identify synteny blocks
| Step | Step designation | Tool | Reference |
| 1 | Identifying homologs | Darwin AllAll | Gonnet et al., 1992 |
| 2a | Identifying orthologs by RSD | Perl script rsd_ortho | FL, this work |
| 2b | Clustering homologs | Perl script famtrans | FL, this work |
| 2c | Breaking bridges | Graph algorithm (Perl graph library) cutbridge | FL, this work |
| 2d | Extracting significant clusters | MCL algorithm | van Dongen, 2000 |
| 2e | Identifying orthologs in evolutionary trees | Perl script tree_ortho | FL, this work |
| 3a | Identifying pairs of adjacent orthologous genes | Querying PostgreSQL database SynteBase | FL, this work |
| 3b | Finding out synteny blocks | Perl script synblock | FL, this work |