\name{ape-internal}
\alias{tree.build}
\alias{f.cherry.yule}
\alias{f.cherry.uniform}
\alias{sortIndex}
\alias{nsca}
\alias{perm.rowscols}
\alias{mant.zstat}
\alias{lower.triang}
\alias{clado.build}
\alias{getDurations}
\alias{getEdgeLengths}
\alias{getExternalParams}
\alias{getNEdges}
\alias{getNFreeParams}
\alias{getRates}
\alias{objFuncLogScale}
\alias{optimTree}
\alias{phylogram}
\alias{prepareTree}
\alias{setTree}
\alias{buildTreeFromPhylo}
\alias{destroyTree}
\alias{getError}
\alias{nEdges}
\alias{nNodes}
\alias{klastorin_nTips}
\alias{getMisawaTajima}
\alias{phylogram.plot}
\alias{cladogram.plot}
\alias{circular.plot}
\alias{unrooted.plot}
\alias{unrooted.xy}
\alias{node.height}
\alias{node.height.clado}
\alias{birth.step}
\alias{death.step}
\alias{ht.move}
\alias{loglik.pop}
\alias{pos.move}
\alias{BOTHlabels}
\alias{chronopl.cv}
\alias{prepareDNA}
\alias{floating.pie.asp}
\alias{checkLabel}
\alias{getMRCA}
\alias{plotCophylo2}
\alias{plotPhyloCoor}
\title{Internal Ape Functions}
\description{
  Internal ape functions.
}
\note{
  These are not to be called by the user (or in some cases are just
  waiting for proper documentation to be written).
}
\keyword{internal}