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Revision as of 18:43, 3 June 2022
Description
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.
Required Modules
Serial
- treepl
System Variables
- HPC_TREEPL_DIR - installation directory