Archive
PhyML 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… Read More
PhyML Benchmarks – Comparison of branch support methods on simulated data sets
Comparison of alRT-based and bootstrap branch supports, using 100 simulated DNA alignments. SH full report – Ki2 full report – Bootstrap full report – Download simulated DNA data sets – Download simulated true trees… Read More
PhyML Benchmarks – aLRT versus bootstrap branch supports
Comparison of alRT-based and bootstrap branch supports, using 100 DNA and protein alignments. See benchmark – Download DNA medium-size data sets – Download protein medium-size data sets Bootstrap and aLRT-SH agreement as a function of the phylogenetic signal: the… Read More
PhyML Benchmarks – Simulated data sets
Comparison of PhyML 3.0 tree search options and RAxML, using 100 simulated DNA data sets. See benchmark – Download simulated DNA data sets – Download simulated true trees Distribution of relative computing times: for the whole set of alignments (100 simulated… Read More
PhyML Benchmarks – Efficiency of filtering strategies
Comparison of distance-based PhyML SPR program (W. Hordijk and O. Gascuel, 2005) and PhyML 3.0 SPR , using different parsimony filtering with various intensities. See DNA benchmark – See protein benchmark – Download DNA medium-size data sets –… Read More
PhyML Benchmarks – Large-size date 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… Read More
PhyML Benchmarks – Medium data sets
Comparison of PhyML 3.0 tree search options and RAxML, using 100 DNA and protein alignments extracted from Treebase. See DNA benchmark – See protein benchmark – Download DNA medium-size data sets – Download protein medium-size data sets… Read More