| Software | Used for | Downloads | Mirror sites |
|---|---|---|---|
| BLAST | BLAST search | NCBI | NCBI EBI |
| getorf | Search for orfs | EMBOSS | Pasteur |
| tRNAscan-SE | Search for tRNA:s | WU | WU |
| Software | Used for | Downloads | Mirror sites |
|---|---|---|---|
| needle and water | Pairwise alignment | EMBOSS | EBI |
| clustalw | Multiple alignment | EBI | EBI |
| Software | Used for | Downloads | Mirror sites |
|---|---|---|---|
| dnadist | Distance method on DNA | Phylip | University of Singapore Pasteur |
| dnapars | Parsimony on DNA | As above | As above |
| dnaml | Likelihood on DNA | As above | As above |
| protdist | Distance method on proteins | As above | As above |
| protpars | Parsimony on proteins | As above | As above |
| neighbor | Neighbor joining algorithm | As above | As above |
| seqboot | Bootstraping | As above | As above |
| consense | Creating consensus trees | As above | As above |
| mix | Parsimony for discrete data | As above | As above |