Jaatha estimates parameters of population
It is freely
available under the terms of the
GNU General Public License (GPL).
Jaatha is developed by Lisha Naduvilezhath, Dirk Metzler and Paul Staab in collaboration with Laura Rose as part of the research project Population genetic methods for inferring adaptation in populations with complex demography within the DFG Research Unit 1078 - Natural selection in structered populations.
The R packages available on CRAN contain Jaatha 2, which is presented in the following manuscript:
Lisha A. Mathew, Paul R. Staab, Laura E. Rose, Dirk Metzler (2013): Why To Account For Finite Sites In Population Genetic Studies And How To Do This With Jaatha 2.0. Ecology and Evolution. [link] - [pdf]
Jaatha is also available from within R (version>=2.15) with the command install.packages("jaatha").
A quick introduction to Jaatha is given in The Jaatha HowTo. Other R packages that are required for the installation of jaatha are "foreach", "ape", "phyclust", and "Rcpp". If you want to use Jaatha with a non-standard type of model and/or simulation software, you can take a look a The Custom Simulator HowTo.
The source code of Jaatha and a bug tracker are available at GitHub.
The function for calculating bootstrap confidence intervals (Jaatha.confidenceIntervals) had a severe bug prior to Version 2.6 that could lead to false intervals. It is highly recommended to rerun the analysis with version 2.6 (or higher) if you used it before.
The R script jaatha_0_2.R contains version 0.2 of Jaatha, which we used in the following article.
L. Naduvilezhath, L.E. Rose, D. Metzler (2011) Jaatha: a fast composite-likelihood approach to estimate demographic parameters Molecular Ecology 20(13):2709-23
The R script jaatha_0_1.R contains version 0.1 of Jaatha, which we used in the following article.
A. Tellier, P. Pfaffelhuber, B. Haubold, L. Naduvilezhath, L. E. Rose, T. Städler, W. Stephan, and D. Metzler (2011) Estimating parameters of speciation models based on refined summaries of the joint site-frequency spectrum PLoS One 6(5): e18155Last modified: 03. Sep. 2014