TABLE 5.
Performance analysis of phylogeny toolsa
| Command line analysis tool (reference) | Concept | Run time (h) | Accuracy (%) | Input format | Output format |
|---|---|---|---|---|---|
| RAxML (191) | Maximum likelihood phylogenetic tree estimator tool; slow but very accurate | 612b | 84.47c | PHYLIP or FASTA | Newick |
| FastTree (163) | Approximately maximum likelihood phylogenetic tree estimator; fast but slightly less accurate | 2.63b | 83.6c | PHYLIP or FASTA | Newick |
| MrBayes (198) | Bayesian-based phylogenetic tree; complex to define models and not user-friendly | ND | ND | NEXUS | NEXUS |
a
All quantitative performance measures were taken from previously reported data, as indicated. The input type for all of these tools is aligned reads/SNPs. ND, no data.
b
Averages for 3 large biological data sets aligned via 3 different methods (TrueAln, PartTree, and Quicktree) (197).
c
Accuracy = 100% − missing branch rates (%) for 3 large biological data sets aligned via 3 different methods (TrueAln, PartTree, and Quicktree) (197).