TreePL

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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. 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





Validation

  • Validate 4/5/2018