ThetaMater is an open source R package for Bayesian estimation of the population parameter theta from genomic data and conducting posterior predictive simulation of population genomic data under the infinite sites model. Long Description (required)
The R package ThetaMater provides a Bayesian framework to simulate posterior probability distributions of θ. At the core of ThetaMater is the infinite-sites likelihood function described in Watterson, 1975 and Tavaré, 1984, which describes the probability distribution of observing k mutations in a sample size of n sequences obtained from a locus with size l (see manual for model description). Integral to ThetaMater is a suite of functions for simulating population genetic data under the infinite sites model, given theta. These functions are used to simulate realistic datasets under the neutral coalescent model, which can be used to identify potential paralogous loci using posterior predictive simulation. With these simulated data, users can identify loci with unexpected patterns (i.e., unlikely mutation counts) of genetic variation. Furthermore, Thetamater includes several functions for simulating datasets that have evolved under models of among-site variation across the genome. https://github.com/radamsRHA/ThetaMater radams@uta.edu
Step 1: Use the attribute tree to add new attributes or remove pre-selected attributes to describe the simulator.
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Summary of Proposed Changes Step 2: Review list of proposed attribute addition(s) and subtraction(s).
Can't Find the Attribute You Are Looking For? If you would like to propose an attribute that you cannot find in the tree above, or if you would like to add a clarification to one or more attributes for this simulator (e.g. a specific file format for attribute /Output/File Format/Other), please list them in the Additional Comment box of the Submit tab .
Summary of Proposed Changes Current Citations/Applications