tree.build

f.cherry.yule

f.cherry.uniform

sortIndex

nsca

perm.rowscols

mant.zstat

lower.triang

clado.build

phylogram.plot

cladogram.plot

circular.plot

unrooted.plot

unrooted.xy

birth.step

death.step

ht.move

loglik.pop

pos.move

BOTHlabels

chronopl.cv

floating.pie.asp

checkLabel

plotCophylo2

plotPhyloCoor

integrateTrapeze

CDF.birth.death

postprocess.prop.part

ONEwise

BaseProportion

C_additive

C_bionj

C_bionjs

C_ewLasso

C_mvr

C_mvrs

C_nj

C_njs

C_pic

C_rTraitCont

C_treePop

C_triangMtd

C_triangMtds

C_ultrametric

C_where

GlobalDeletionDNA

DNAbin2indelblock

SegSites

bipartition

delta_plot

dist_dna

dist_nodes

mat_expo

me_b

me_o

neworder_phylo

neworder_pruningwise

node_depth

node_depth_edgelength

node_height

node_height_clado

prop_part

rawStreamToDNAbin

seq_root2tip

treeBuildWithTokens

polar2rect

rect2polar

CountBipartitionsFromTrees

bitsplits_multiPhylo

bitsplits_phylo

racine

renumeroteArbre

calculeC

getSumSquare

getMLHessian

getREMLHessian

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 allelic and nucleotide data, 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. 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

ape-internal function

Internal Ape Functions

ape-internal: Internal Ape Functions

Description

Arguments