tree.build

f.cherry.yule

f.cherry.uniform

sortIndex

nsca

perm.rowscols

mant.zstat

lower.triang

clado.build

getDurations

getEdgeLengths

getExternalParams

getNEdges

getNFreeParams

getRates

objFuncLogScale

optimTree

phylogram

prepareTree

setTree

buildTreeFromPhylo

destroyTree

getError

nEdges

nNodes

nTips

getMisawaTajima

phylogram.plot

cladogram.plot

unrooted.plot

unrooted.xy

node.height

node.height.clado

birth.step

death.step

ht.move

loglik.pop

pos.move

BOTHlabels

chronopl.cv

prepare.dna

floating.pie.asp

checkLabel

getMRCA

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, nucleotide diversity,
  generalized skyline plots, estimation of absolute evolutionary rates
  and clock-like trees using non-parametric rate smoothing and penalized
  likelihood, classifying genes in trees using the Klastorin-Misawa-Tajima
  approach. Phylogeny estimation can be done with the NJ and ML methods.

Emmanuel Paradis

Analyses of Phylogenetics and Evolution

ape-internal function

Internal Ape Functions

ape-internal: Internal Ape Functions

Description

Arguments