\name{ape-defunct}
\alias{klastorin}
+\alias{mlphylo}
+\alias{DNAmodel}
+\alias{sh.test}
\alias{heterozygosity}
\alias{H}
\alias{nuc.div}
}
\usage{
klastorin(phy)
+mlphylo(x, phy, model = DNAmodel(), search.tree = FALSE,
+ quiet = FALSE, value = NULL, fixed = FALSE)
+DNAmodel(model = "K80", partition = 1,
+ ncat.isv = 1, invar = FALSE,
+ equal.isv = TRUE, equal.invar = 1)
+sh.test(..., x, model = DNAmodel(), B = 100)
heterozygosity(x, variance = FALSE)
H(x, variance = FALSE)
nuc.div(x, variance = FALSE, pairwise.deletion = FALSE)
and this helped to clear some internal C code (this function may be
put back with a different coding).
+ \code{mlphylo}, \code{DNAmodel} and \code{sh.test} have been removed:
+ see the package \pkg{phangorn} for a much better implementation of
+ these methods (and others).
+
\code{heterozygosity}, \code{nuc.div}, \code{theta.h}, \code{theta.k}
and \code{theta.s} have been moved to \pkg{pegas}.
}