AetLTR                  LTR retrotransposons in _Aegilops tauschii_
AlyLTR                  LTR retrotransposons in _Arabidopsis lyrata_
EstDynamics             Estimate TE dynamics using mismatch data
MasterGene              Implements the master gene model in Marchani et
                        al (2009)
MatrixModel             Implements the matrix model in Promislow et al
                        (1999)
PlotFamilies            Plot the age distributions or insertion rates
                        for multiple families.
SensitivityPlot         Generate sensitivity plots
TE                      TE: Insertion/Deletion Dynamics for
                        Transposable Elements
nbLackOfFitKL           Calcualte the KL divergence of a negative
                        binomial fit to the mismatch data.
print.TEfit             Print a TEfit or TEfit2 object
