perm.rowscols

phylogram.plot

cladogram.plot

circular.plot

unrooted.plot

unrooted.xy

BOTHlabels

floating.pie.asp

plotPhyloCoor

postprocess.prop.part

ONEwise

reorderRcpp

polar2rect

rect2polar

neworder_phylo

neworder_pruningwise

node_depth

node_depth_edgelength

node_height

node_height_clado

seq_root2tip

<p>Internal <span class="pkg">ape</span> functions which are undocumented but still exported
  because called by other packages. Use with care!</p>

internal

ape-internal

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

Emmanuel Paradis

Analyses of Phylogenetics and Evolution

Simon Blomberg

Ben Bolker

Joseph Brown

Julien Claude

Hoa Sien Cuong

Richard Desper

Gilles Didier

Benoit Durand

Julien Dutheil

RJ Ewing

Olivier Gascuel

Thomas Guillerme

Christoph Heibl

Anthony Ives

Bradley Jones

Franz Krah

Daniel Lawson

Vincent Lefort

Pierre Legendre

Jim Lemon

Eric Marcon

Rosemary McCloskey

Johan Nylander

Rainer Opgen-Rhein

Andrei-Alin Popescu

Manuela Royer-Carenzi

Klaus Schliep

Korbinian Strimmer

Damien de Vienne

ape-internal function

Internal Ape Functions — ape-internal

Internal Ape Functions

ape-internal: Internal Ape Functions

Description

Arguments