treePL

Description

treepl website

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.

Environment Modules

Run module spider treepl to find out what environment modules are available for this application.

Environment Variables

• HPC_TREEPL_DIR - installation directory
• HPC_TREEPL_BIN - executable directory

Categories

biology, phylogenetics