Table 1.
List of tools currently integrated in NGPhylogeny.fr
| Step | Tool name | New | Version | Dataset size ability | ‘One click’ | ‘Advanced’ | ‘A la carte’ | ‘Stand-alone’ |
|---|---|---|---|---|---|---|---|---|
| MSA | Clustal Ω (16) | Yes | 1.2.4.1 | Very large | ✓ | ✓ | ||
| MSA | MAFFT (2) | Yes | 7.407 | Large | ✓ | ✓ | ✓ | ✓ |
| MSA | MUSCLE (17) | Up | 3.8.37 | Medium | ✓ | ✓ | ||
| AC | Gblocks (18) | - | 0.91b | Very large | ✓ | ✓ | ||
| AC | trimAl (21) | Yes | 1.4.1 | Very large | ✓ | ✓ | ||
| AC | BMGE (19) | Yes | 1.12 | Medium | ✓ | ✓ | ✓ | ✓ |
| AC | Noisy (20) | Yes | 1.5.12.1 | Small | ✓ | ✓ | ||
| TI (Fast max-likelihood) | FastTree (22) | Yes | 2.1.10 | Very large | ✓ | ✓ | ✓ | ✓ |
| TI (Distance) | FastME (4) | Yes | 2.1.6.1 | Large | ✓ | ✓ | ✓ | ✓ |
| TI (Parsimony) | TNT (23) | Yes | 1.5.0a | Large | ✓ | ✓ | ||
| TI (Max-likelihood) | PhyML (3) | Up | 3.1 | Medium | ✓ | ✓ | ✓ | ✓ |
| TI (PhyML+MS) | PhyML (3)+SMS (24) | Yes | 1.8.1 | Medium | ✓ | ✓ | ✓ | ✓ |
| TI (Bayesian) | MrBayes (25) | Yes | 3.2.6 | Small | ✓ | ✓ | ||
| TV | Newick Utilities (26) | Yes | 1.6 | Large | ✓ | ✓ | ✓ | ✓ |
| BS | BOOSTER (5) | Yes | 0.2.4 | Large | ✓ | ✓ | ✓ |
Step: MSA for multiple sequence alignment, AC for alignment curation, TI for tree inference, TV for tree visualization, BS for branch support, and MS for model selection. New: Yes for new tools, Up for updated tools and - for tools already present in Phylogeny.fr. Dataset size ability: dataset dimension able to be analyzed by each tool, very large (typically >10 000 sequences), large (>5000), medium (>1000), small (≤1000). ‘One click’, ‘Advanced’, ‘A la carte’ and ‘Stand-alone’: tools that are available in each run mode.