Table 1.
Main tools available on Phylogeny.fr
| Program | Function | Input | Output | Speed | Current limitations | Use |
|---|---|---|---|---|---|---|
| Blastall 2.2.17 | Sequence searching | Raw, FASTA | FASTA | Fast | None | Advanced and A la Carte |
| MUSCLE 3.6 | Multiple alignment | FASTA, EMBL/Uniprot, GenBank | FASTA, Clustal, PHYLIP | Fast | <200 sequences | All modes Large dataset |
| T-Coffee 4.97 | Multiple alignment | FASTA, EMBL/Uniprot, GenBank | FASTA, Clustal, PHYLIP, others | Very slow | <50 sequences < 2000 sites | A la Carte Small dataset |
| 3DCoffee 4.97 | Multiple alignment using structural information | FASTA, EMBL/Uniprot, GenBank | FASTA, Clustal, PHYLIP, others | Very slow | <50 sequences <2000 sites | A la Carte Small dataset |
| ClustalW 1.83 | Multiple alignment | FASTA, EMBL/Uniprot, GenBank | FASTA, Clustal, PHYLIP | Fast | <200 sequences | A la Carte Large dataset |
| Gblocks 0.91b | Alignment refinement | FASTA | FASTA, Clustal, PHYLIP | Fast | None | All modes Large dataset |
| PhyML 3.0 | Phylogeny using maximum likelihood | FASTA, Clustal, PHYLIP, EMBL, PAUP*/Nexus | Newick | Fast to slow | (sequence size) × (number of taxa)2 < 10 000 000 | All modes Medium to large dataset |
| NONA 2.0 | DNA phylogeny using parsimony | FASTA, Clustal, PHYLIP, EMBL, PAUP*/Nexus | Newick | Fast to slow | (sequence size) × (number of taxa)2 < 10 000 000 | A la Carte Medium to large datasets |
| Protpars 3.66 | Protein phylogeny using parsimony | FASTA, Clustal, PHYLIP, EMBL, PAUP*/Nexus | Newick | Very slow | (sequence size) × (number of taxa)2 < 10 000 000 | A la Carte Small to medium dataset |
| Dnadist Protdist BioNJ NJ PHYLYP 3.66 | Phylogeny using distances | FASTA, Clustal, PHYLIP, EMBL, PAUP*/Nexus | Newick | Fast | None | A la Carte Large dataset |
| Bootstrap with PhyML, NONA, Protpars | Estimations of clade supports | FASTA, Clustal, PHYLIP, EMBL, PAUP*/Nexus | Newick | Very slow | <100 replicates | Advanced and A la Carte Small to medium datasets |
| Bootstrap with distance methods | Estimations of clade supports | FASTA, Clustal, PHYLIP, EMBL, PAUP*/Nexus | Newick | Slow | <500 replicates | A la Carte Medium to large datasets |
| TreeDyn 198 | Tree rendering | Newick | PNG, PDF, TGF | Fast | None | All modes |
| Drawgram 3.66 | Various tree shapes rendering | Newick | PNG, PDF | Fast | None | A la Carte |
| Drawtree 3.66 | Unrooted tree rendering | Newick | PNG, PDF | Fast | None | A la Carte |
With fast programs Phylogeny.fr displays the results within a few minutes or less. Slow programs require about one hour or so, but their results are still displayed on-line, while the results of very slow programs are sent by email.