PhyML 3.0 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

Simulated data sets

Bootstrap and aLRT-SH agreement as a function of the phylogenetic signal: the phylogenetic signal is measured by the number of sites (with less than 10% gaps or missing values) times the median of internal branch lengths. This roughly corresponds to the expected number of substitutions supporting any given internal branch. Branch support agreement equals the proportion of branches with both SH-like support > 0.90 and bootstrap support > 0.75.

Data sets

The benchmark contains 50 protein alignments and 50 DNA alignments.