treePL is a method for calculating divergence time estimates using penalized likelihood (Sanderson, 2002) on large phylogenies. Penalized likelihood uses a semi-parametric approach that allows for different rates on different branches but has a smoothing parameter, set using cross-validation, that affects how much rate differences over the tree are penalized. This approach attempts to overcome the problem of local minima, a problem amplified by including more taxa. This approach provides performance comparable with or better than that of the existing software including r8s, PATHd8 and BEAST.
module spider treepl to find out what environment modules are available for this application.
- HPC_TREEPL_DIR - installation directory