API for ape
Analyses of Phylogenetics and Evolution

Global functions
$.multiPhylo	Man page
$<-.multiPhylo	Man page
+.phylo	Man page
.AAString2AAbin	Source code
.CDF.birth.death2	Source code
.DNAString2DNAbin	Source code
.PlotPhyloEnv	Man page
.buildDegeneracyMatrix	Source code
.bydir.html	Source code
.c_phylo_single	Source code
.check.tip.label	Source code
.cladoBuild	Source code
.cladoBuildWithTokens	Source code
.compressTipLabel	Man page Source code
.di2multi_ape	Source code
.dist.topo.score	Source code
.errorAlignment	Source code
.evonet2phylo	Source code
.getCase	Source code
.getProb4rtree	Source code
.getRHOetINT	Source code
.getSEs	Source code
.getSeparatorTaxaLabels	Source code
.getTreesFromDotdotdot	Source code
.is.rooted_ape	Source code
.is.ultrametric_ape	Source code
.makeMultiPhyloFromObj	Source code
.makePhylo	Source code
.matchDataPhylo	Source code
.multi2di_ape	Source code
.parse.annotations.file	Source code
.reorder_ape	Source code
.treeBuild	Source code
.treeBuildWithTokens	Source code
.uncompressTipLabel	Man page Source code
.unroot_ape	Source code
.write.efa	Source code
.write.tree2	Source code
AAbin	Man page
AAsubst	Man page Source code
AIC.ace	Man page Source code
BOTHlabels	Man page Source code
CADM	Man page
CADM.global	Man page
CADM.post	Man page
CDF.birth.death	Source code
DNAbin	Man page
DNAbin2indel	Man page Source code
FastME	Man page
Ftab	Man page Source code
GC.content	Man page Source code
HP.links	Man page
Initialize.corPhyl	Man page Source code
LTT	Man page Source code
LargeNumber	Man page Source code
MPR	Man page Source code
Moran.I	Man page Source code
Nedge	Man page Source code
Nedge.evonet	Man page Source code
Nedge.multiPhylo	Man page Source code
Nedge.phylo	Man page Source code
Nnode	Man page Source code
Nnode.multiPhylo	Man page Source code
Nnode.phylo	Man page Source code
Ntip	Man page Source code
Ntip.multiPhylo	Man page Source code
Ntip.phylo	Man page Source code
ONEwise	Man page Source code
SDM	Man page Source code
SHORTwise	Man page Source code
Xplor	Man page Source code
Xplorefiles	Man page Source code
[.AAbin	Man page
[.DNAbin	Man page
[.multiPhylo	Man page
[<-.multiPhylo	Man page
[[.multiPhylo	Man page
[[<-.multiPhylo	Man page
`$.multiPhylo`	Source code
`$<-.multiPhylo`	Source code
`+.phylo`	Source code
`CADM.global`	Source code
`CADM.post`	Source code
`[<-.multiPhylo`	Source code
`[[<-.multiPhylo`	Source code
abbreviateGenus	Man page Source code
ace	Man page Source code
add.scale.bar	Man page Source code
additive	Man page Source code
alex	Man page Source code
all.equal.DNAbin	Man page Source code
all.equal.phylo	Man page Source code
alview	Man page Source code
anova.ace	Man page Source code
ape	Man page
ape-package	Man page
apetools	Man page
arecompatible	Man page Source code
as.AAbin	Man page Source code
as.AAbin.AAMultipleAlignment	Man page Source code
as.AAbin.AAString	Man page Source code
as.AAbin.AAStringSet	Man page Source code
as.AAbin.character	Man page Source code
as.AAbin.list	Man page Source code
as.DNAbin	Man page Source code
as.DNAbin.DNAMultipleAlignment	Man page Source code
as.DNAbin.DNAString	Man page Source code
as.DNAbin.DNAStringSet	Man page Source code
as.DNAbin.PairwiseAlignmentsSingleSubject	Man page Source code
as.DNAbin.alignment	Man page Source code
as.DNAbin.character	Man page Source code
as.DNAbin.list	Man page Source code
as.alignment	Man page Source code
as.bitsplits	Man page Source code
as.bitsplits.prop.part	Man page Source code
as.character.AAbin	Man page Source code
as.character.DNAbin	Man page Source code
as.evonet	Man page Source code
as.evonet.phylo	Man page Source code
as.hclust.phylo	Man page Source code
as.igraph	Man page
as.igraph.evonet	Man page Source code
as.igraph.phylo	Man page Source code
as.list.AAbin	Man page Source code
as.list.DNAbin	Man page Source code
as.matching	Man page Source code
as.matching.phylo	Man page Source code
as.matrix.AAbin	Man page Source code
as.matrix.DNAbin	Man page Source code
as.network.evonet	Man page Source code
as.network.phylo	Man page Source code
as.networx.evonet	Man page Source code
as.phyDat.AAbin	Man page Source code
as.phylo	Man page
as.phylo.default	Man page Source code
as.phylo.evonet	Man page Source code
as.phylo.formula	Man page Source code
as.phylo.hclust	Man page Source code
as.phylo.matching	Man page Source code
as.phylo.phylog	Man page Source code
as.prop.part	Man page Source code
as.prop.part.bitsplits	Man page Source code
axisPhylo	Man page Source code
balance	Man page Source code
base.freq	Man page Source code
bd.ext	Man page Source code
bd.time	Man page Source code
binaryPGLMM	Man page Source code
binaryPGLMM.sim	Man page Source code
bind.tree	Man page Source code
bionj	Man page Source code
bionjs	Man page Source code
bipartition2	Source code
biplot.pcoa	Man page
bird.families	Man page
bird.orders	Man page
birth.step	Source code
birthdeath	Man page Source code
bitsplits	Man page Source code
boot.phylo	Man page Source code
branching.times	Man page Source code
bydir	Man page Source code
c.AAbin	Man page Source code
c.DNAbin	Man page Source code
c.multiPhylo	Man page Source code
c.phylo	Man page Source code
calculeC	Source code
calculeC_ABM	Source code
calculeC_OU	Source code
carnivora	Man page
cbind.AAbin	Man page Source code
cbind.DNAbin	Man page Source code
checkAlignment	Man page Source code
checkLabel	Man page Source code
checkValidPhylo	Man page Source code
cherry	Man page Source code
chiroptera	Man page
chronoMPL	Man page Source code
chronopl	Man page Source code
chronopl.cv	Source code
chronos	Man page Source code
chronos.control	Man page Source code
circular.plot	Man page Source code
cladewise	Man page Source code
cladogram.plot	Man page Source code
clustal	Man page Source code
clustalomega	Man page
coalescent.intervals	Man page Source code
coalescent.intervals.default	Man page Source code
coalescent.intervals.phylo	Man page Source code
coef.corBlomberg	Man page Source code
coef.corBrownian	Man page Source code
coef.corGrafen	Man page Source code
coef.corMartins	Man page Source code
coef.corPagel	Man page Source code
collapse.singles	Man page Source code
collapsed.intervals	Man page Source code
compar.cheverud	Man page Source code
compar.gee	Man page Source code
compar.lynch	Man page Source code
compar.ou	Man page Source code
comparePhylo	Man page Source code
complement	Man page Source code
compute.brlen	Man page Source code
compute.brtime	Man page Source code
consensus	Man page Source code
cophenetic.phylo	Man page Source code
cophyloplot	Man page Source code
corBlomberg	Man page Source code
corBrownian	Man page Source code
corClasses	Man page
corGrafen	Man page Source code
corMartins	Man page Source code
corMatrix.corBlomberg	Man page Source code
corMatrix.corBrownian	Man page Source code
corMatrix.corGrafen	Man page Source code
corMatrix.corMartins	Man page Source code
corMatrix.corPagel	Man page Source code
corPagel	Man page Source code
corPhyl	Man page
corphylo	Man page Source code
correlogram.formula	Man page Source code
countBipartitions	Man page Source code
cynipids	Man page
data.nex	Man page
dbd	Man page Source code
dbdTime	Man page Source code
death.step	Source code
def	Man page Source code
degree	Man page Source code
degree.evonet	Man page Source code
degree.phylo	Man page Source code
del.colgapsonly	Man page Source code
del.gaps	Man page Source code
del.rowgapsonly	Man page Source code
delta.plot	Man page Source code
deviance.ace	Man page Source code
di2multi	Man page Source code
di2multi.multiPhylo	Man page Source code
di2multi.phylo	Man page
dist.aa	Man page Source code
dist.dna	Man page Source code
dist.gene	Man page Source code
dist.nodes	Man page Source code
dist.topo	Man page Source code
diversi.gof	Man page Source code
diversi.time	Man page Source code
diversity.contrast.test	Man page Source code
dnds	Man page Source code
drawSupportOnEdges	Man page Source code
drop.fossil	Man page Source code
drop.tip	Man page Source code
drop.tip.multiPhylo	Man page Source code
drop.tip.phylo	Man page Source code
drop1.compar.gee	Man page Source code
dyule	Man page Source code
edgelabels	Man page Source code
edges	Man page Source code
editFileExtensions	Man page Source code
efastats	Man page Source code
estimate.dates	Man page Source code
estimate.mu	Man page Source code
evonet	Man page Source code
ewLasso	Man page Source code
extract.clade	Man page Source code
extract.popsize	Man page Source code
f.cherry.uniform	Source code
f.cherry.yule	Source code
fancyarrows	Man page Source code
fastme	Man page
fastme.bal	Man page Source code
fastme.ols	Man page Source code
find.skyline.epsilon	Man page Source code
floating.pie.asp	Man page Source code
gammaStat	Man page Source code
getAnnotationsGenBank	Man page Source code
getMLHessian	Source code
getMRCA	Man page Source code
getREMLHessian	Source code
getSumSquare	Source code
gopher.D	Man page
has.singles	Man page Source code
hivtree	Man page
hivtree.newick	Man page
hivtree.table	Man page
howmanytrees	Man page Source code
ht.move	Source code
identify.phylo	Man page Source code
image.AAbin	Man page Source code
image.DNAbin	Man page Source code
integrateTrapeze	Source code
is.binary	Man page Source code
is.binary.multiPhylo	Man page Source code
is.binary.phylo	Man page Source code
is.binary.tree	Man page Source code
is.compatible	Man page Source code
is.compatible.bitsplits	Man page Source code
is.monophyletic	Man page Source code
is.rooted	Man page Source code
is.rooted.multiPhylo	Man page Source code
is.rooted.phylo	Man page
is.ultrametric	Man page Source code
is.ultrametric.multiPhylo	Man page Source code
is.ultrametric.phylo	Man page Source code
keep.tip	Man page Source code
keep.tip.multiPhylo	Man page Source code
keep.tip.phylo	Man page Source code
kronoviz	Man page Source code
label2table	Man page Source code
labels.AAbin	Man page Source code
labels.DNAbin	Man page Source code
ladderize	Man page Source code
latag2n	Man page Source code
letterconf	Man page Source code
lice.D	Man page
lines.popsize	Man page Source code
lines.skyline	Man page Source code
lmorigin	Man page
lmorigin.ex1	Man page
lmorigin.ex2	Man page
logLik.ace	Man page Source code
loglik.pop	Source code
ltt.coplot	Man page Source code
ltt.lines	Man page Source code
ltt.plot	Man page Source code
ltt.plot.coords	Man page Source code
makeChronosCalib	Man page Source code
makeLabel	Man page Source code
makeLabel.DNAbin	Man page Source code
makeLabel.character	Man page Source code
makeLabel.multiPhylo	Man page Source code
makeLabel.phylo	Man page Source code
makeNodeLabel	Man page Source code
mant.zstat	Source code
mantel.test	Man page Source code
mat3	Man page
mat5M3ID	Man page
mat5Mrand	Man page
matching	Man page
matexpo	Man page Source code
mcconwaysims.test	Man page Source code
mcmc.popsize	Man page Source code
mixedFontLabel	Man page Source code
mltt.plot	Man page Source code
mrca	Man page Source code
mst	Man page Source code
multi2di	Man page Source code
multi2di.multiPhylo	Man page Source code
multi2di.phylo	Man page
multiphylo	Man page
muscle	Man page
muscle5	Man page Source code
mvr	Man page Source code
mvrs	Man page Source code
new2old.phylo	Man page Source code
next.calib	Source code
nexus2DNAbin	Man page Source code
nj	Man page Source code
njs	Man page Source code
node.dating	Man page
node.depth	Man page Source code
node.depth.edgelength	Man page Source code
node.height	Man page Source code
node_depth	Man page
node_depth_edgelength	Man page
node_height	Man page
node_height_clado	Man page
nodelabels	Man page Source code
nodepath	Man page Source code
nsca	Source code
old2new.phylo	Man page Source code
parafit	Man page
pcoa	Man page Source code
perm.rowscols	Man page Source code
phydataplot	Man page Source code
phylo	Man page
phylogram.plot	Man page Source code
phymltest	Man page Source code
pic	Man page Source code
pic.ortho	Man page Source code
plot.correlogram	Man page Source code
plot.correlogramList	Man page Source code
plot.evonet	Man page Source code
plot.mst	Man page Source code
plot.multiPhylo	Man page Source code
plot.phylo	Man page Source code
plot.phylo.extra	Man page
plot.phymltest	Man page Source code
plot.popsize	Man page Source code
plot.prop.part	Man page Source code
plot.skyline	Man page Source code
plot.varcomp	Man page Source code
plotBreakLongEdges	Man page Source code
plotCophylo2	Source code
plotPhyloCoor	Man page
plotTreeTime	Man page Source code
polar2rect	Man page Source code
pos.move	Source code
postorder	Man page Source code
postprocess.prop.part	Man page Source code
predict.compar.gee	Man page Source code
print.AAbin	Man page Source code
print.DNAbin	Man page Source code
print.LargeNumber	Man page Source code
print.ace	Man page Source code
print.binaryPGLMM	Man page Source code
print.birthdeath	Man page Source code
print.bitsplits	Man page Source code
print.chronos	Man page Source code
print.compar.gee	Man page Source code
print.comparePhylo	Man page Source code
print.corphylo	Man page Source code
print.evonet	Man page Source code
print.lmorigin	Man page
print.multiPhylo	Man page Source code
print.parafit	Man page
print.phylo	Man page Source code
print.phymltest	Man page Source code
print.prop.part	Man page Source code
prop.clades	Man page Source code
prop.part	Man page Source code
prop_part2	Source code
r.squared	Source code
rDNAbin	Man page Source code
rTraitCont	Man page Source code
rTraitDisc	Man page Source code
rTraitMult	Man page Source code
racine	Source code
rbdtree	Man page Source code
rbind.AAbin	Man page Source code
rbind.DNAbin	Man page Source code
rcoal	Man page Source code
read.FASTA	Man page Source code
read.GenBank	Man page Source code
read.caic	Man page Source code
read.dna	Man page Source code
read.evonet	Man page Source code
read.fastq	Man page Source code
read.gff	Man page Source code
read.nexus	Man page Source code
read.nexus.data	Man page
read.tree	Man page Source code
reconstruct	Man page
rect2polar	Man page Source code
relabel	Source code
renumeroteArbre	Source code
reorder.evonet	Man page Source code
reorder.multiPhylo	Man page Source code
reorder.phylo	Man page Source code
reorderRcpp	Man page Source code
replace.single.quotes	Source code
richness.yule.test	Man page Source code
ring	Man page Source code
rlineage	Man page Source code
rmtopology	Man page Source code
rmtree	Man page Source code
root	Man page Source code
root.multiPhylo	Man page Source code
root.phylo	Man page Source code
rotate	Man page Source code
rotateConstr	Man page Source code
rphylo	Man page Source code
rtopology	Man page Source code
rtree	Man page Source code
rtt	Man page
seg.sites	Man page Source code
seq_root2tip	Man page
sigmasq	Source code
skyline	Man page Source code
skyline.coalescentIntervals	Man page Source code
skyline.collapsedIntervals	Man page Source code
skyline.phylo	Man page Source code
skylineplot	Man page Source code
skylineplot.deluxe	Man page Source code
slowinskiguyer.test	Man page Source code
solveAmbiguousBases	Man page Source code
sort.bitsplits	Man page Source code
sortIndex	Source code
speciesTree	Man page Source code
str.multiPhylo	Man page Source code
stree	Man page Source code
stripLabel	Man page Source code
subtreeplot	Man page Source code
subtrees	Man page Source code
summary.phylo	Man page Source code
summary.phymltest	Man page Source code
summary.prop.part	Man page Source code
tcoffee	Man page Source code
tidy.xy	Source code
tiplabels	Man page Source code
trans	Man page Source code
treePop	Man page Source code
trex	Man page Source code
triangMtd	Man page Source code
triangMtds	Man page Source code
ultrametric	Man page Source code
unique.multiPhylo	Man page Source code
unroot	Man page Source code
unroot.multiPhylo	Man page Source code
unroot.phylo	Man page Source code
unrooted.xy	Man page Source code
updateLabel	Man page Source code
updateLabel.AAbin	Man page Source code
updateLabel.DNAbin	Man page Source code
updateLabel.character	Man page Source code
updateLabel.data.frame	Man page Source code
updateLabel.evonet	Man page Source code
updateLabel.matrix	Man page Source code
updateLabel.phylo	Man page Source code
varCompPhylip	Man page Source code
varcomp	Man page Source code
vcv	Man page Source code
vcv.corPhyl	Man page Source code
vcv.phylo	Man page Source code
vcv2phylo	Man page
weight.taxo	Man page Source code
weight.taxo2	Man page Source code
where	Man page Source code
which.edge	Man page Source code
woodmouse	Man page
write.FASTA	Man page Source code
write.dna	Man page Source code
write.evonet	Man page Source code
write.nexus	Man page Source code
write.nexus.data	Man page Source code
write.tree	Man page Source code
yule	Man page Source code
yule.cov	Man page Source code
yule.time	Man page Source code
zoom	Man page Source code