Av. LogLk rank | Delta>5 | P-value<0.05 | Av. RF distance | |

PhyML 2.4.5 | 3.975 | 4 | 0 | 0.102 |

PhyML 3.0 NNI | 3.59 | 3 | 0 | 0.100 |

PhyML 3.0 SPR | 3.705 | 0 | 0 | 0.100 |

PhyML 3.0 BEST | 3.075 | 0 | 0 | 0.097 |

PhyML 3.0 RAND | 2.8 | 0 | 0 | 0.097 |

RAxML | 3.855 | 0 | 0 | 0.097 |

- PhyML_2.4.5

Previous version of PhyML, optimizing the topology with simultaneous NNIs (original PhyML algorithm), and using a BioNJ starting tree. - PhyML 3.0 NNI

PhyML, optimizing the topology with both simultaneous NNIs (as in original PhyML algorithm) and refined NNIs with 5-edge-length optimization, and using a BioNJ starting tree. - PhyML 3.0 SPR

PhyML, optimizing the topology with SPR (and NNI 3.0) operations, and using a BioNJ starting tree. - PhyML 3.0 BEST

PhyML, best tree obtained by PHYML_NNI and PHYML_SPR. - PhyML 3.0 BEST RANDOM

PhyML, adding to the BEST option 5 SPR tree searches using random starting trees, output is the best of the 7 inferred trees. - RAxML

RAxML version 7.0. To obtain comparable results, the tree likelihood has been re-optimized by PhyML, keeping the topology but fitting all numerical parameters.

- Computing time ranks

The six methods are ranked for each of the alignments, based on the computing time. First rank contains methods with computing time ranging from the best (B) computing time to 1.25 X B (i.e. nearly best computing time). Remaining methods are ranked in the same way, until all methods are ranked. Ties are accounted for; e.g. if the first and second group contains 2 methods each, the ranks will be 1.5 ( (1+2)/2 ) and 3.5 ( (3+4)/2 ). To summarize these results, we provide the median and average ranks for all alignments. - LogLK ranks

The six methods are ranked for each of the alignments using a similar principle, based on the tree likelihood. Ranks account for ties, just as with log-likelihood values. Moreover, we provide the median and average ranks for all DNA and protein alignments. - Robinson and Foulds distances

RF is the Robinson and Foulds (bipartition) distance between the best topology and the given topology. - Robinson and Foulds ranks

The six methods are ranked for each of the alignments using a similar principle, based on the RF distance with the true tree. First rank contains all methods which find the same best topology. And so on. Moreover, we provide the median and average ranks for all alignments. - Delta>5

Another variable of interest is the number of times a method fails to find a phylogeny which log-likelihood is close to the highest log-likelihood found by any of the methods being compared. We thus counted the number of data sets for which the log-likelihoods returned by a given method was smaller than the highest log-likelihood found on the corresponding alignments minus 5.0. While this boundary of 5.0 points of log-likelihood is arbitrary, we believe that it provides a simple and practical way to tell the methods apart at first sight. - SH tests

We used the Shimoidara-Hasegawa (SH) test to assess the statistical significance of the likelihood differences. Every result displays the P-value between its logLk and the logLk of the best result for the same data. As a summary, we provide the number of times each method is significatively worst than the best one.