Insertion/Deletion Dynamics for Transposable Elements
Estimate TE dynamics using mismatch data
Implements the master gene model in Marchani et al (2009)
Implements the matrix model in Promislow et al (1999)
Calcualte the KL divergence of a negative binomial fit to the mismatch...
Plot the age distributions or insertion rates for multiple families.
Print a TEfit or TEfit2 object
Generate sensitivity plots
TE: Insertion/Deletion Dynamics for Transposable Elements
Provides functions to estimate the insertion and deletion rates of transposable element (TE) families. The estimation of insertion rate consists of an improved estimate of the age distribution that takes into account random mutations, and an adjustment by the deletion rate. A hypothesis test for a uniform insertion rate is also implemented. This package implements the methods proposed in Dai et al (2018).