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$.multiPhylo multiphylo
$<-.multiPhylo multiphylo
+.phylo bind.tree
.compressTipLabel c.phylo
.uncompressTipLabel c.phylo
AAbin AAbin
AAsubst AAbin
abbreviateGenus label2table
ace ace
add.scale.bar add.scale.bar
additive additive
AIC.ace ace
alex alex
all.equal.DNAbin all.equal.DNAbin
all.equal.phylo all.equal.phylo
alview alview
anova.ace ace
ape ape-package
apetools apetools
arecompatible is.compatible
as.AAbin AAbin
as.AAbin.character AAbin
as.AAbin.list AAbin
as.alignment as.alignment
as.bitsplits as.bitsplits
as.bitsplits.prop.part as.bitsplits
as.character.AAbin AAbin
as.character.DNAbin as.alignment
as.DNAbin as.alignment
as.DNAbin.alignment as.alignment
as.DNAbin.character as.alignment
as.DNAbin.DNAMultipleAlignment as.alignment
as.DNAbin.DNAString as.alignment
as.DNAbin.DNAStringSet as.alignment
as.DNAbin.list as.alignment
as.DNAbin.PairwiseAlignmentsSingleSubject as.alignment
as.evonet evonet
as.evonet.phylo evonet
as.hclust.phylo as.phylo
as.igraph as.phylo
as.igraph.evonet evonet
as.igraph.phylo as.phylo
as.list.AAbin AAbin
as.list.DNAbin DNAbin
as.matching as.matching
as.matching.phylo as.matching
as.matrix.AAbin AAbin
as.matrix.DNAbin DNAbin
as.network.evonet evonet
as.network.phylo as.phylo
as.networx.evonet evonet
as.phyDat.AAbin AAbin
as.phylo as.phylo
as.phylo.evonet evonet
as.phylo.formula as.phylo.formula
as.phylo.hclust as.phylo
as.phylo.matching as.matching
as.phylo.phylog as.phylo
as.prop.part as.bitsplits
as.prop.part.bitsplits as.bitsplits
axisPhylo axisPhylo
balance balance
base.freq base.freq
BaseProportion ape-internal
bd.ext bd.ext
bd.time bd.time
binaryPGLMM binaryPGLMM
binaryPGLMM.sim binaryPGLMM
bind.tree bind.tree
bionj bionj
bionjs njs
bipartition ape-internal
bipartition2 ape-internal
biplot.pcoa pcoa
bird.families bird.families
bird.orders bird.orders
birth.step ape-internal
birthdeath birthdeath
bitsplits as.bitsplits
bitsplits_multiPhylo ape-internal
bitsplits_phylo ape-internal
boot.phylo boot.phylo
BOTHlabels ape-internal
branching.times branching.times
bydir apetools
c.AAbin AAbin
c.DNAbin DNAbin
c.multiPhylo c.phylo
c.phylo c.phylo
CADM CADM.global
CADM.global CADM.global
CADM.post CADM.global
calculeC ape-internal
calculeC_ABM ape-internal
calculeC_OU ape-internal
carnivora carnivora
cbind.DNAbin DNAbin
CDF.birth.death ape-internal
checkAlignment checkAlignment
checkLabel ape-internal
checkValidPhylo checkValidPhylo
cherry cherry
chiroptera chiroptera
chronoMPL chronoMPL
chronopl chronopl
chronopl.cv ape-internal
chronos chronos
chronos.control chronos
circular.plot ape-internal
cladewise reorder.phylo
cladoBuild ape-internal
cladoBuildWithTokens ape-internal
cladogram.plot ape-internal
clustal clustal
clustalomega clustal
coalescent.intervals coalescent.intervals
coalescent.intervals.default coalescent.intervals
coalescent.intervals.phylo coalescent.intervals
coef.corBlomberg corBlomberg
coef.corBrownian corBrownian
coef.corGrafen corGrafen
coef.corMartins corMartins
coef.corPagel corPagel
collapse.singles collapse.singles
collapsed.intervals collapsed.intervals
compar.cheverud compar.cheverud
compar.gee compar.gee
compar.lynch compar.lynch
compar.ou compar.ou
complement trans
compute.brlen compute.brlen
compute.brtime compute.brtime
consensus consensus
cophenetic.phylo cophenetic.phylo
cophyloplot cophyloplot
corBlomberg corBlomberg
corBrownian corBrownian
corClasses corClasses
corGrafen corGrafen
corMartins corMartins
corMatrix.corBlomberg corBlomberg
corMatrix.corBrownian corBrownian
corMatrix.corGrafen corGrafen
corMatrix.corMartins corMartins
corMatrix.corPagel corPagel
corPagel corPagel
corPhyl corClasses
corphylo corphylo
correlogram.formula correlogram.formula
countBipartitions as.bitsplits
CountBipartitionsFromTrees ape-internal
cynipids cynipids
C_additive ape-internal
C_bionj ape-internal
C_bionjs ape-internal
C_ewLasso ape-internal
C_mvr ape-internal
C_mvrs ape-internal
C_nj ape-internal
C_njs ape-internal
C_pic ape-internal
C_rTraitCont ape-internal
C_treePop ape-internal
C_triangMtd ape-internal
C_triangMtds ape-internal
C_ultrametric ape-internal
C_where ape-internal
data.nex cynipids
dbd dbd
dbdTime dbd
death.step ape-internal
def def
del.colgapsonly del.gaps
del.gaps del.gaps
del.rowgapsonly del.gaps
delta.plot delta.plot
delta_plot ape-internal
deviance.ace ace
di2multi multi2di
di2multi.multiPhylo multi2di
di2multi.phylo multi2di
dist.aa AAbin
dist.dna dist.dna
dist.gene dist.gene
dist.nodes cophenetic.phylo
dist.topo dist.topo
dist_dna ape-internal
dist_nodes ape-internal
diversi.gof diversi.gof
diversi.time diversi.time
diversity.contrast.test diversity.contrast.test
DNAbin DNAbin
DNAbin2indel DNAbin2indel
DNAbin2indelblock ape-internal
drawSupportOnEdges plot.phyloExtra
drop.fossil rlineage
drop.tip drop.tip
drop1.compar.gee compar.gee
dyule dbd
edgelabels nodelabels
edges edges
editFileExtensions apetools
estimate.dates node.dating
estimate.mu node.dating
evonet evonet
ewLasso ewLasso
extract.clade drop.tip
extract.popsize mcmc.popsize
f.cherry.uniform ape-internal
f.cherry.yule ape-internal
fancyarrows edges
FastME fastme
fastme fastme
fastme.bal fastme
fastme.ols fastme
find.skyline.epsilon skyline
floating.pie.asp ape-internal
Ftab base.freq
gammaStat gammaStat
GC.content base.freq
getMLHessian ape-internal
getMRCA mrca
getREMLHessian ape-internal
getSumSquare ape-internal
GlobalDeletionDNA ape-internal
glsABM ape-internal
glsBM ape-internal
glsOUv1 ape-internal
glsOUv2 ape-internal
gopher.D parafit
has.singles collapse.singles
hivtree hivtree
hivtree.newick hivtree
hivtree.table hivtree
howmanytrees howmanytrees
HP.links parafit
ht.move ape-internal
identify.phylo identify.phylo
image.AAbin AAbin
image.DNAbin image.DNAbin
Initialize.corPhyl Initialize.corPhyl
integrateTrapeze ape-internal
is.binary is.binary.tree
is.binary.multiPhylo is.binary.tree
is.binary.phylo is.binary.tree
is.binary.tree is.binary.tree
is.compatible is.compatible
is.compatible.bitsplits is.compatible
is.monophyletic is.monophyletic
is.rooted root
is.rooted.multiPhylo root
is.rooted.phylo root
is.ultrametric is.ultrametric
is.ultrametric.multiPhylo is.ultrametric
is.ultrametric.phylo is.ultrametric
kronoviz kronoviz
label2table label2table
labels.AAbin AAbin
labels.DNAbin DNAbin
ladderize ladderize
lice.D parafit
lines.popsize mcmc.popsize
lines.skyline skylineplot
lmorigin lmorigin
lmorigin.ex1 lmorigin
lmorigin.ex2 lmorigin
logLik.ace ace
loglik.pop ape-internal
lower.triang ape-internal
LTT LTT
ltt.coplot ltt.plot
ltt.lines ltt.plot
ltt.plot ltt.plot
ltt.plot.coords ltt.plot
makeChronosCalib chronos
makeLabel makeLabel
makeLabel.character makeLabel
makeLabel.DNAbin makeLabel
makeLabel.multiPhylo makeLabel
makeLabel.phylo makeLabel
makeNodeLabel makeNodeLabel
mant.zstat ape-internal
mantel.test mantel.test
mat3 mat3
mat5M3ID mat5M3ID
mat5Mrand mat5Mrand
matching as.matching
matexpo matexpo
mat_expo ape-internal
mcconwaysims.test mcconwaysims.test
mcmc.popsize mcmc.popsize
me_b ape-internal
me_o ape-internal
mixedFontLabel mixedFontLabel
mltt.plot ltt.plot
Moran.I MoranI
MPR MPR
mrca mrca
mst mst
multi2di multi2di
multi2di.multiPhylo multi2di
multi2di.phylo multi2di
multiphylo multiphylo
muscle clustal
mvr mvr
mvrs mvr
Nedge summary.phylo
Nedge.evonet evonet
Nedge.multiPhylo summary.phylo
Nedge.phylo summary.phylo
new2old.phylo as.phylo
neworder_phylo ape-internal
neworder_pruningwise ape-internal
nj nj
njs njs
Nnode summary.phylo
Nnode.multiPhylo summary.phylo
Nnode.phylo summary.phylo
node.dating node.dating
node.depth node.depth
node.depth.edgelength node.depth
node.height node.depth
nodelabels nodelabels
nodepath nodepath
node_depth ape-internal
node_depth_edgelength ape-internal
node_height ape-internal
node_height_clado ape-internal
nsca ape-internal
Ntip summary.phylo
Ntip.multiPhylo summary.phylo
Ntip.phylo summary.phylo
old2new.phylo as.phylo
ONEwise ape-internal
parafit parafit
pcoa pcoa
perm.rowscols ape-internal
phydataplot phydataplot
phylo read.tree
phylogram.plot ape-internal
phymltest phymltest
pic pic
pic.ortho pic.ortho
plot.correlogram plot.correlogram
plot.correlogramList plot.correlogram
plot.evonet evonet
plot.mst mst
plot.multiPhylo plot.phylo
plot.phylo plot.phylo
plot.phylo.extra plot.phyloExtra
plot.phymltest phymltest
plot.popsize mcmc.popsize
plot.prop.part boot.phylo
plot.skyline skylineplot
plot.varcomp plot.varcomp
plotBreakLongEdges plot.phyloExtra
plotCophylo2 ape-internal
plotPhyloCoor ape-internal
plotTreeTime plotTreeTime
polar2rect ape-internal
pos.move ape-internal
postorder reorder.phylo
postprocess.prop.part ape-internal
predict.compar.gee compar.gee
print.AAbin AAbin
print.ace ace
print.binaryPGLMM binaryPGLMM
print.birthdeath birthdeath
print.bitsplits as.bitsplits
print.chronos chronos
print.compar.gee compar.gee
print.corphylo corphylo
print.DNAbin DNAbin
print.evonet evonet
print.lmorigin lmorigin
print.multiPhylo print.phylo
print.parafit parafit
print.phylo print.phylo
print.phymltest phymltest
print.prop.part boot.phylo
prop.clades boot.phylo
prop.part boot.phylo
prop_part2 ape-internal
racine ape-internal
rawStreamToDNAbin ape-internal
rbdtree rlineage
rbind.DNAbin DNAbin
rcoal rtree
read.caic read.caic
read.dna read.dna
read.evonet evonet
read.FASTA read.dna
read.fastq read.dna
read.GenBank read.GenBank
read.gff read.gff
read.nexus read.nexus
read.nexus.data read.nexus.data
read.tree read.tree
reconstruct reconstruct
rect2polar ape-internal
renumeroteArbre ape-internal
reorder.evonet evonet
reorder.multiPhylo reorder.phylo
reorder.phylo reorder.phylo
reorderRcpp ape-internal
richness.yule.test richness.yule.test
ring phydataplot
rlineage rlineage
rmtree rtree
root root
root.multiPhylo root
root.phylo root
rotate rotate
rotateConstr rotate
rphylo rlineage
rTraitCont rTraitCont
rTraitDisc rTraitDisc
rTraitMult rTraitMult
rtree rtree
rtt rtt
SDM SDM
seg.sites seg.sites
SegSites ape-internal
seq_root2tip ape-internal
skyline skyline
skyline.coalescentIntervals skyline
skyline.collapsedIntervals skyline
skyline.phylo skyline
skylineplot skylineplot
skylineplot.deluxe skylineplot
slowinskiguyer.test slowinskiguyer.test
sort.bitsplits as.bitsplits
sortIndex ape-internal
speciesTree speciesTree
str.multiPhylo print.phylo
stree stree
stripLabel label2table
subtreeplot subtreeplot
subtrees subtrees
summary.phylo summary.phylo
summary.phymltest phymltest
summary.prop.part boot.phylo
tcoffee clustal
tiplabels nodelabels
trans trans
trans_DNA2AA ape-internal
treeBuild ape-internal
treeBuildWithTokens ape-internal
treePop treePop
trex trex
triangMtd triangMtd
triangMtds triangMtd
ultrametric additive
unique.multiPhylo unique.multiPhylo
unroot root
unroot.multiPhylo root
unroot.phylo root
unrooted.plot ape-internal
unrooted.xy ape-internal
varcomp varcomp
varCompPhylip varCompPhylip
vcv vcv.phylo
vcv.corPhyl vcv.phylo
vcv.phylo vcv.phylo
vcv2phylo vcv2phylo
weight.taxo weight.taxo
weight.taxo2 weight.taxo
where where
which.edge which.edge
woodmouse woodmouse
write.dna write.dna
write.evonet evonet
write.nexus write.nexus
write.nexus.data write.nexus.data
write.tree write.tree
Xplor apetools
Xplorefiles apetools
yule yule
yule.cov yule.cov
yule.time yule.time
zoom zoom
[.AAbin AAbin
[.DNAbin DNAbin
[.multiPhylo multiphylo
[<-.multiPhylo multiphylo
[[.multiPhylo multiphylo
[[<-.multiPhylo multiphylo
_ape_bipartition2 ape-internal
_ape_prop_part2 ape-internal
_ape_reorderRcpp ape-internal
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