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
.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
.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.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.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
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
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
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
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
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
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
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
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
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
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
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
ape documentation built on April 25, 2021, 9:06 a.m.