Molecular Dating with Penalized Likelihood

Molecular Dating with Penalized Likelihood uses Find Lambda and run PL, two phylogenetic methods that: 1) allow a rough calculation of lambda (smoothing parameter) and 2) given a best lambda, calculate nodal ages of a tree using penalized likelihood methods.  

Quick Start

• To use Molecular Dating with Penalized Likelihood , upload your data .phy format.
• Resources:
  • Sanderson, M. J. (2002) Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Molecular Biology and Evolution, 19, 101--109.

Test Data

All files are located in the Community Data directory of the iPlant Discovery Environment at the following path:

Community Data > iplantcollaborative > example_data > molecular_dating_with_penalized_likelihood

Input File(s)

• Use randomTree.phy from randomTree.phy as a test input file.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below. 

If running mode is:

1. "Find best Lambda only", use default settings
2. "Calculate Penalized Likelihood", Lambda = 0.001, sequence length = 100
3. "Find best lambda and calculate PL", use default settings

Output File(s)

• Expect a chrono.phy file as output if using PL. 

Tool Source for App

• FindLambdaAndRunPL.R\
• http://rss.acs.unt.edu/Rdoc/library/ape/html/chronopl.html