Difference between revisions of "TreePL"

Jump to navigation Jump to search
(Created page with "Category:SoftwareCategory:BioinformaticsCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|treepl}} |{{#vardefine:url|https://github.com/bla...")
Line 82: Line 82:
<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
* Validate 4/5/2018

Revision as of 20:42, 5 April 2018


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


  • treepl

System Variables

  • HPC_{{#uppercase:treepl}}_DIR - installation directory


  • Validate 4/5/2018