API for gjuggler/ape
Analyses of Phylogenetics and Evolution

Global functions
$.multiPhylo	Man page
$<-.multiPhylo	Man page
+.phylo	Man page
.compressTipLabel	Man page
.uncompressTipLabel	Man page
AIC.ace	Man page
BOTHlabels	Man page
CADM	Man page
CADM.global	Man page
CADM.post	Man page
CDF.birth.death	Man page
DNAbin	Man page
DNAmodel	Man page
Ftab	Man page
GC.content	Man page
H	Man page
HP.links	Man page
Initialize.corPhyl	Man page
MPR	Man page
Moran.I	Man page
NPRS.criterion	Man page
Nedge	Man page
Nnode	Man page
Ntip	Man page
[.DNAbin	Man page
[.multiPhylo	Man page
[<-.multiPhylo	Man page
[[.multiPhylo	Man page
[[<-.multiPhylo	Man page
ace	Man page
add.scale.bar	Man page
all.equal.phylo	Man page
anova.ace	Man page
ape	Man page
ape-defunct	Man page
ape-package	Man page
as.DNAbin	Man page
as.DNAbin.alignment	Man page
as.DNAbin.character	Man page
as.DNAbin.list	Man page
as.alignment	Man page
as.character.DNAbin	Man page
as.hclust.phylo	Man page
as.list.DNAbin	Man page
as.matching	Man page
as.matching.phylo	Man page
as.matrix.DNAbin	Man page
as.phylo	Man page
as.phylo.formula	Man page
as.phylo.hclust	Man page
as.phylo.matching	Man page
as.phylo.phylog	Man page
axisPhylo	Man page
balance	Man page
base.freq	Man page
bd.ext	Man page
bd.time	Man page
bind.tree	Man page
bionj	Man page
biplot.pcoa	Man page
bird.families	Man page
bird.orders	Man page
birth.step	Man page
birthdeath	Man page
boot.phylo	Man page
branching.times	Man page
c.DNAbin	Man page
c.multiPhylo	Man page
c.phylo	Man page
carnivora	Man page
cbind.DNAbin	Man page
checkLabel	Man page
cherry	Man page
chiroptera	Man page
chronoMPL	Man page
chronogram	Man page
chronopl	Man page
chronopl.cv	Man page
circular.plot	Man page
clado.build	Man page
cladogram.plot	Man page
coalescent.intervals	Man page
coalescent.intervals.default	Man page
coalescent.intervals.phylo	Man page
coef.corBlomberg	Man page
coef.corBrownian	Man page
coef.corGrafen	Man page
coef.corMartins	Man page
coef.corPagel	Man page
collapse.singles	Man page
collapsed.intervals	Man page
compar.cheverud	Man page
compar.gee	Man page
compar.lynch	Man page
compar.ou	Man page
compute.brlen	Man page
consensus	Man page
cophenetic.phylo	Man page
cophyloplot	Man page
corBlomberg	Man page
corBrownian	Man page
corClasses	Man page
corGrafen	Man page
corMartins	Man page
corMatrix.corBlomberg	Man page
corMatrix.corBrownian	Man page
corMatrix.corGrafen	Man page
corMatrix.corMartins	Man page
corMatrix.corPagel	Man page
corPagel	Man page
corPhyl	Man page
correlogram.formula	Man page
cynipids	Man page
data.nex	Man page
death.step	Man page
del.gaps	Man page
delta.plot	Man page
deviance.ace	Man page
di2multi	Man page
dist.dna	Man page
dist.gene	Man page
dist.nodes	Man page
dist.topo	Man page
diversi.gof	Man page
diversi.time	Man page
drop.fossil	Man page
drop.tip	Man page
drop1.compar.gee	Man page
edgelabels	Man page
edges	Man page
evolve.phylo	Man page
extract.clade	Man page
extract.popsize	Man page
f.cherry.uniform	Man page
f.cherry.yule	Man page
fancyarrows	Man page
fastme	Man page
fastme.bal	Man page
fastme.ols	Man page
find.skyline.epsilon	Man page
floating.pie.asp	Man page
gammaStat	Man page
getMRCA	Man page
gopher.D	Man page
heterozygosity	Man page
hivtree	Man page
hivtree.newick	Man page
hivtree.table	Man page
howmanytrees	Man page
ht.move	Man page
identify.phylo	Man page
integrateTrapeze	Man page
is.binary.tree	Man page
is.monophyletic	Man page
is.rooted	Man page
is.ultrametric	Man page
klastorin	Man page
labels.DNAbin	Man page
ladderize	Man page
landplants	Man page
landplants.newick	Man page
lice.D	Man page
lines.popsize	Man page
lines.skyline	Man page
lmorigin	Man page
lmorigin.ex1	Man page
lmorigin.ex2	Man page
logLik.ace	Man page
loglik.pop	Man page
lower.triang	Man page
ltt.lines	Man page
ltt.plot	Man page
makeLabel	Man page
makeLabel.DNAbin	Man page
makeLabel.character	Man page
makeLabel.multiPhylo	Man page
makeLabel.phylo	Man page
makeNodeLabel	Man page
mant.zstat	Man page
mantel.test	Man page
mat3	Man page
mat5M3ID	Man page
mat5Mrand	Man page
matexpo	Man page
mcmc.popsize	Man page
mixedFontLabel	Man page
mlphylo	Man page
mltt.plot	Man page
mrca	Man page
mst	Man page
multi2di	Man page
multiphylo	Man page
new2old.phylo	Man page
nj	Man page
node.depth	Man page
node.height	Man page
node.height.clado	Man page
nodelabels	Man page
nsca	Man page
nuc.div	Man page
old2new.phylo	Man page
opsin	Man page
opsin.newick	Man page
parafit	Man page
pcoa	Man page
perm.rowscols	Man page
phylogram.plot	Man page
phymltest	Man page
pic	Man page
pic.ortho	Man page
plot.ancestral	Man page
plot.correlogram	Man page
plot.correlogramList	Man page
plot.mst	Man page
plot.multiPhylo	Man page
plot.phylo	Man page
plot.phymltest	Man page
plot.popsize	Man page
plot.prop.part	Man page
plot.skyline	Man page
plot.varcomp	Man page
plotCophylo2	Man page
plotPhyloCoor	Man page
pos.move	Man page
print.DNAbin	Man page
print.ace	Man page
print.birthdeath	Man page
print.compar.gee	Man page
print.lmorigin	Man page
print.multiPhylo	Man page
print.parafit	Man page
print.phylo	Man page
print.phymltest	Man page
print.prop.part	Man page
prop.clades	Man page
prop.part	Man page
rTraitCont	Man page
rTraitDisc	Man page
ratogram	Man page
rbdtree	Man page
rbind.DNAbin	Man page
rcoal	Man page
read.GenBank	Man page
read.caic	Man page
read.dna	Man page
read.nexus	Man page
read.nexus.data	Man page
read.tree	Man page
reorder.phylo	Man page
rlineage	Man page
rmtree	Man page
root	Man page
rotate	Man page
rtree	Man page
seg.sites	Man page
sh.test	Man page
skyline	Man page
skyline.coalescentIntervals	Man page
skyline.collapsedIntervals	Man page
skyline.phylo	Man page
skylineplot	Man page
skylineplot.deluxe	Man page
sortIndex	Man page
speciesTree	Man page
str.multiPhylo	Man page
stree	Man page
subtreeplot	Man page
subtrees	Man page
summary.phylo	Man page
summary.phymltest	Man page
summary.prop.part	Man page
theta.h	Man page
theta.k	Man page
theta.s	Man page
tiplabels	Man page
tree.build	Man page
unique.multiPhylo	Man page
unroot	Man page
unrooted.plot	Man page
unrooted.xy	Man page
varCompPhylip	Man page
varcomp	Man page
vcv	Man page
vcv.corPhyl	Man page
vcv.phylo	Man page
weight.taxo	Man page
weight.taxo2	Man page
which.edge	Man page
woodmouse	Man page
write.dna	Man page
write.nexus	Man page
write.nexus.data	Man page
write.tree	Man page
yule	Man page
yule.cov	Man page
yule.time	Man page
zoom	Man page