PhyML 3.0 Benchmarks

CAT methods

Comparison between programs (RAxML and FastTree) using the CAT approximation (Stamatakis, 2006) of the Γ4 mixture model (Yang, 1993), and PhyML 3.0 using the full standard Γ4 model.

See DNA benchmark - See protein benchmark - Download DNA medium-size data sets - Download protein medium-size data sets

Branch supports Branch supports

Distribution of relative computing times: for each of the 2 sets of alignments (50 DNA and 50 protein medium-size alignments) we measured the base-2 logarithm of the ratio of the computing time of the given method, and that of the fastest approach with the corresponding alignment. Thus, a log-ratio equals to X corresponds to a method being 2^X times slower than the fastest approach.

DNAAv. LogLk rankDelta>5P-value<0.05Av. RF distance
PhyML 3.0 NNI3.213360.2711
PhyML 3.0 SPR1.36100.0692
RAxML CAT2.19700.2058
FastTree reoptimized3.243550.2585

PROTEINAv. LogLk rankDelta>5P-value<0.05Av. RF distance
PhyML 3.0 NNI2.821910.2144
PhyML 3.0 SPR1.8300.0641
RAxML CAT2.06210.108
FastTree reoptimized3.312620.2762

Comparison of log-likelihoods on 50 DNA and 50 protein medium-size data sets. The column ‘Av. LogLk rank’ gives the average log-likelihood ranks for the different methods. These ranks are corrected by taking into account information on tree topologies. ‘Delta>5’ gives the number of cases (among 50) for which the drops of log-likelihood between the method of interest and the highest log-likelihood for the corresponding data set is greater than 5. The column ‘p-value<0.05’ displays the number of cases for which the difference of log-likelihood when comparing the method of interest to the corresponding highest log-likelihood is statistically significant (SH test). The ‘Av. RF distance’ values are the average Robinson and Foulds topological distances between the trees estimated by the method of interest and the corresponding most likely trees (0 corresponds to identical trees, while 1 means that the two trees do not have any clade in common).


4 programs and options have been compared.


Resulting trees are compared regarding topology, log-likelihood and computing time.