  Massively parallel DNA sequencing techniques are rapidly changing the
dynamics of phylogenetic study design by exponentially increasing the discovery
of phylogenetically useful loci. This increase in the number of phylogenetic
markers potentially provides researchers the opportunity to select subsets of
loci best-addressing particular phylogenetic hypotheses based on objective
measures of performance over different time scales. Investigators may also want
to determine the power of particular phylogenetic markers relative to each
other. However, currently available tools are designed to evaluate a small
number of markers and are not well-suited to screening hundreds or thousands of
candidate loci across the genome. TAPIR is an alternative implementation of
Townsend's estimate of phylogenetic informativeness (PI) that enables rapid
estimation and summary of PI when applied to data sets containing hundreds to
thousands of candidate, phylogenetically informative loci.
