A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
Authors: Stéphane Guindon (Auckland University, New Zealand) and Olivier Gascuel (LIRMM, Montpellier, France)
PHYML is a software implementing a new method for building phylogenies from DNA and protein sequences using maximum likelihood. Data sets can be analysed under several models of evolution (JC69, K80, F81, F84, HKY85, TN93 and GTR for nucleotides and Dayhoff, JTT, mtREV, WAG and DCMut for amino acids). A discrete-gamma model (Yang, 1994) is implemented to accommodate rate variation among sites. Invariable sites can also be taken into account. PHYML has been compared to several other softwares using extensive simulations. The results indicate that its topological accuracy is at least as high as that of fastDNAml, while being much faster.