tree.build

f.cherry.yule

f.cherry.uniform

sort.index

nsca

get.dna

perm.rowscols

mant.zstat

lower.triang

clado.build

getDurations

getEdgeLengths

getExternalParams

getNEdges

getNFreeParams

getRates

objFuncLogScale

optimTree

phylogram

prepareTree

setTree

buildTreeFromHclust

buildTreeFromPhylo

destroyTree

edgeLengthsForPhylo

getError

getHclust

getPhylo

leftNodesForHclust

lowerNodesForPhylo

nEdges

nNodes

nodeHeightsForHclust

nTips

rightNodesForHclust

tipLabelsForPhylo

upperNodesForPhylo

getMisawaTajima

phylogram.plot

cladogram.plot

unrooted.plot

unrooted.xy

node.height

node.height.clado

birth.step

death.step

ht.move

loglik.pop

pos.move

internal

ape-internal

Ape provides functions for reading, writing, plotting,
  and manipulating phylogenetic trees, analyses of comparative data
  in a phylogenetic framework, analyses of diversification and
  macroevolution, computing distances from allelic and nucleotide
  data, reading nucleotide sequences, and several tools such as
  Mantel's test, computation of minimum spanning tree, the population
  parameter theta based on various approaches, generalized skyline plots,
  estimation of absolute evolutionary rates and clock-like
  trees using non-parametric rate smoothing, conversion of APE trees
  to and from hclust objects and for classifying genes in trees using
  the Klastorin-Misawa-Tajima approach.

Emmanuel Paradis

Analyses of Phylogenetics and Evolution

ape-internal function

Internal Ape Functions

ape-internal: Internal Ape Functions

Description

Arguments