Speed comparison of pplacerand RAxML's EPA algorithm. Time to place 10,000 16 s rRNA reads of median length 198 nt onto a reference phylogenetic tree, with a 1287 nt reference alignment. "Γ model" refers to a four-category gamma model of rate heterogeneity , and "CAT" is an approximation which chooses a single rate for each site . Tests run on an Intel Xeon @ 2.33 Ghz.
Matsen et al. BMC Bioinformatics 2010 11:538 doi:10.1186/1471-2105-11-538