| TE {TE} | R Documentation |
TE: Insertion/Deletion Dynamics for Transposable Elements
Description
TE package for analyzing insertion/deletion dynamics for transposable elements
Details
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. This
package includes functions EstDynamics and EstDynamics2 for
analyzing the TE divergence, and visualization functions such as
PlotFamilies and SensitivityPlot.
This package implements the methods proposed in Dai et al (2018+).
Author(s)
Xiongtao Dai xdai@iastate.edu, Hao Wang Jan Dvorak Jeffrey Bennetzen Hans-Georg Mueller
Maintainer: Xiongtao Dai xdai@iastate.edu
References
Luo, Ming-Cheng, et al. (2017) "Genome sequence of the progenitor of the wheat D genome Aegilops tauschii." Nature 551.7681.
Dai, X., Wang, H., Dvorak, J., Bennetzen, J., Mueller, H.-G. (2018). "Birth and Death of LTR Retrotransposons in Aegilops tauschii". Genetics