TABLE 5

Performance analysis of phylogeny toolsa

Command line analysis tool (reference)ConceptRun time (h)Accuracy (%)Input formatOutput format
RAxML (191)Maximum likelihood phylogenetic tree estimator tool; slow but very accurate612b84.47cPHYLIP or FASTANewick
FastTree (163)Approximately maximum likelihood phylogenetic tree estimator; fast but slightly less accurate2.63b83.6cPHYLIP or FASTANewick
MrBayes (198)Bayesian-based phylogenetic tree; complex to define models and not user-friendlyNDNDNEXUSNEXUS
  • 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).