ATGC: Phyml 3.0 benchmarks

PhyML 3.0 Benchmarks

Large-size data sets

Comparison of PhyML 3.0 tree search options and RAxML, using 20 DNA and protein alignments extracted from Treebase.

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

Distribution of relative computing times: for each of the 2 sets of alignments (10 DNA and 10 protein large-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; e.g. with DNA alignments PhyML 2.4.5 NNI is basically twice faster than PhyML 3.0 NNI, but both are pretty much the same with protein alignments.

DNA	Av. LogLk rank	Delta>5	P-value<0.05	Av. RF distance
PhyML 2.4.5	3.5	10	8	0.47
PhyML 3.0 NNI	3.5	10	7	0.46
PhyML 3.0 SPR	1.4	3	0	0.15
RAxML	1.6	5	1	0.23

PROTEIN	Av. LogLk rank	Delta>5	P-value<0.05	Av. RF distance
PhyML 2.4.5	3.45	7	3	0.24
PhyML 3.0 NNI	2.65	6	3	0.20
PhyML 3.0 SPR	2.75	7	0	0.18
RAxML	1.14	0	0	0.0

Comparison of log-likelihoods on 10 DNA and 10 protein large-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 10) for which the difference 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).

Data sets

The benchmark contains 10 protein alignments and 10 DNA alignments.

DNA alignments
We selected the 10 most recent alignments from Treebase with at least 300 sequences, without any limitation on the number of sites and sequences.
Protein alignments
We selected the 10 most recent alignments from Treebase with at least 40 sequences, without any limitation on the number of sites and sequences.

Programs

4 programs and options have been compared. All programs were configured with the GTR model for DNA sequences, with WAG for proteins, and with 4 discrete gamma rate categories (alpha estimated from the data).

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.
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.

Results

Resulting trees are compared regarding topology, log-likelihood and computing time, using the same criteria as with medium-size data sets.

Computing time ranks
The four 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 DNA and protein alignments.
Topology ranks
The four methods are ranked for each of the alignments using a similar principle, based on the tree likelihood. First rank contains all methods which find the same best topology. And so on. 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.
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.