API for phangorn
Phylogenetic Reconstruction and Analysis

Global functions
AICc Man page Source code
AICc.pml Source code
Ancestors Man page Source code
BIC.pml Source code
BranchAndBound Man page
CI Man page Source code
Children Man page Source code
Descendants Man page Source code
E_Intruder Source code
E_Intruder_2 Source code
KF.dist Man page Source code
Laurasiatherian Man page
NJ Man page Source code
NJ_old Source code
PNJ Man page Source code
RF.dist Man page Source code
RF0 Source code
RI Man page Source code
RSS Source code
Rx Source code
SH.test Man page Source code
SH.tmp Source code
SHORTwise Source code
SOWH.test Man page Source code
SPR.dist Man page Source code
SPR1 Source code
SPR2 Source code
Siblings Man page Source code
UNJ Man page Source code
acctran Man page Source code
acgt2ry Man page Source code
add.one Source code
add.tips Man page Source code
addConfidences Man page Source code
addConfidences.networx Source code
addConfidences.phylo Source code
addConfidences.splits Source code
addConfidencesMultiPhylo Source code
addEdge Source code
addOne Source code
addOneTree Source code
addTrivialSplits Man page Source code
add_tiplabels Source code
aggr Source code
aic.weights Source code
allAncestors Source code
allChildren Source code
allChildrenCPP Source code
allCircularSplits Man page Source code
allDescCPP Source code
allDescendants Man page Source code
allKids Source code
allSitePattern Man page Source code
allSplits Man page Source code
allTrees Man page Source code
ancestral.pars Man page Source code
ancestral.pml Man page Source code
ancestral2phyDat Source code
ancstat Source code
anova.pml Source code
as.AAbin.phyDat Man page Source code
as.DNAbin.phyDat Man page Source code
as.Matrix Man page Source code
as.Matrix.splits Man page Source code
as.MultipleAlignment Man page Source code
as.MultipleAlignment.phyDat Man page Source code
as.bitsplits.splits Man page Source code
as.character.phyDat Man page Source code
as.data.frame.phyDat Man page Source code
as.matrix.splits Man page Source code
as.networx Man page Source code
as.networx.phylo Man page Source code
as.networx.splits Man page Source code
as.phyDat Man page Source code
as.phyDat.DNAbin Man page Source code
as.phyDat.MultipleAlignment Man page Source code
as.phyDat.alignment Man page Source code
as.phyDat.character Man page Source code
as.phyDat.data.frame Man page Source code
as.phyDat.factor Man page Source code
as.phyDat.matrix Man page Source code
as.phylo.splits Man page Source code
as.prop.part.splits Man page Source code
as.splits Man page Source code
as.splits.multiPhylo Man page Source code
as.splits.networx Man page Source code
as.splits.phylo Man page Source code
as.splits.prop.part Source code
bab Man page Source code
baseFreq Man page Source code
bip Source code
bipCPP Source code
bipart Source code
bipartCPP Source code
bipartition Source code
bootstrap.phyDat Man page Source code
bootstrap.pml Man page Source code
c.phyDat Man page
c.splits Man page Source code
cbind.phyDat Man page Source code
changeEdge Source code
changeEdgeLength Source code
changeOrder Source code
checkLabels Source code
chloroplast Man page
circNetwork Source code
cladeMatrix Source code
cladePar Man page Source code
closest.edge Source code
closest.node Source code
coalSpeciesTree Man page Source code
codon2dna Man page Source code
comp Source code
comp2 Source code
compareSplits Source code
compatible Man page Source code
compatible2 Source code
compatible3 Source code
compatible_2 Source code
compressSites Source code
consensusNet Man page Source code
constSitePattern Source code
coords Man page Source code
coph Source code
cophenetic.networx Man page Source code
cophenetic.splits Man page Source code
countCycles Source code
createLabel Man page Source code
cyclicSplits Source code
dec2Bin Source code
dec2bin Source code
delta.quartet Source code
delta.score Man page Source code
densiTree Man page Source code
descAll Source code
designAll Source code
designSplits Man page Source code
designStar Source code
designTree Man page Source code
designUltra Source code
designUnrooted Source code
designUnrooted2 Source code
dfactorial Man page
discrete.gamma Man page Source code
dist.hamming Man page Source code
dist.logDet Man page Source code
dist.ml Man page Source code
dist.p Man page Source code
dist.superTree Source code
distC Source code
distanceHadamard Man page Source code
distinct.splits Man page Source code
diversity Man page Source code
dl Source code
dltmp Source code
dn Source code
dna2codon Man page Source code
dropNode Source code
dropTip Source code
edQ Source code
edQ2 Source code
edQt Man page Source code
edgeLabels Source code
edgeLengthIndex Source code
fast.fitch Source code
fast.table Source code
fast.table2 Source code
fhm Man page Source code
fit.fitch Source code
fit.sankoff Source code
fit.sankoffNew Source code
fitch Man page Source code
fitch.nni Source code
fitch.spr Source code
fitch.spr2 Source code
fitchCoding2ambiguous Source code
fitchCoding2ambiguous2 Source code
fn.quartet Source code
fn.quartet2 Source code
fnodesNew2 Source code
fnodesNew5 Source code
fs Source code
fs3 Source code
fun.rf Source code
fun.spr Source code
genlight2phyDat Man page Source code
getAges Source code
getClans Man page Source code
getClips Man page Source code
getCols Source code
getDiv Source code
getDiversity Man page Source code
getE Source code
getIndex Source code
getModelAA Source code
getOrder Source code
getOrdering Source code
getOrderingNN Source code
getOrderingNN2 Source code
getOrderingNN4 Source code
getP Source code
getRoot Man page Source code
getRows Source code
getSlices Man page Source code
getd2P Source code
getd2P2 Source code
getdP Source code
getdP2 Source code
h2st Man page Source code
h4st Man page Source code
hC Source code
hadamard Man page Source code
identify.networx Man page Source code
image.phyDat Man page Source code
index.nni Source code
index2edge Source code
index2tree Source code
index2tree2 Source code
indexNNI Source code
indexNNI2 Source code
indexNNI3 Source code
kSPR Source code
kart2kreis Source code
kart2kugel Source code
kf0 Source code
kf1 Source code
kf2 Source code
kreis2kart Source code
kugel2kart Source code
ldfactorial Man page Source code
lento Man page Source code
likelihoodRatchet Source code
lli Man page Source code
logLik.pml Source code
logLik.pmlMix Source code
logLik.pmlPart Source code
lowerBound Source code
mRF Source code
mRF2 Source code
makePart Source code
map_duplicates Man page Source code
mast Man page Source code
mast.fit Source code
matchEdges Source code
matchSplits Man page Source code
maxCladeCred Man page Source code
midpoint Man page Source code
midpoint.multiPhylo Man page Source code
midpoint.phylo Man page Source code
modelTest Man page Source code
moving_average Source code
mpr Source code
mpr.help Source code
mrca.phylo Man page Source code
mrca2 Source code
multiphyDat2pmlPart Man page Source code
my.supertree Source code
n_nni Source code
neighborNet Man page Source code
neighborNet2 Source code
networx Man page
new2old.phyDat Source code
nni Man page Source code
nnin Source code
nnls.networx Man page Source code
nnls.phylo Man page Source code
nnls.splits Man page Source code
nnls.tree Man page Source code
nodeHeight Source code
old2new.phyDat Source code Source code
oneOf4 Source code
oneWise Source code
one_nnin Source code
optCycle Source code
optEdgeMulti Source code
optNNI Source code
optW Source code
optWPen Source code
optim.fitch Source code
optim.parsimony Man page Source code
optim.pml Man page Source code
optim.quartet Source code
optim.quartet2 Source code
optim.sankoff Source code
optimBf Source code
optimCodon Source code
optimEdge Source code
optimGamma Source code
optimInv Source code
optimMixBf Source code
optimMixEdge Source code
optimMixInv Source code
optimMixQ Source code
optimMixRate Source code
optimPartBf Source code
optimPartEdge Source code
optimPartGamma Source code
optimPartInv Source code
optimPartNNI Source code
optimPartQGeneral Source code
optimQ Source code
optimQuartet Source code
optimRate Source code
optimRooted Source code
optimW Source code
orderNNI Source code
p2dna Source code
pBound Source code
pace Man page
parsimony Man page Source code
parsimony.plot Source code
parsinfo Source code
path.dist Man page Source code
pd0 Source code
pd1 Source code
pd2 Source code
phangorn Man page
phangorn-internal Man page
phangorn-package Man page
phangornParseFormula Source code
phyDat Man page Source code
phyDat.AA Source code
phyDat.DNA Source code
phyDat.codon Source code
phyDat.default Source code
phyDat2MultipleAlignment Man page
phyDat2alignment Man page Source code
phylo Source code
plot.networx Man page Source code
plot.pml Source code
plot.pmlCluster Source code
plot.pmlPart Source code
plot2D Source code
plotAnc Man page Source code
plotBS Man page Source code
plotRGL Source code
pml Man page Source code
pml.control Man page Source code
pml.fit Man page Source code
pml.fit4 Source code
pml.free Man page Source code
pml.init Man page Source code
pml.move Source code
pml.nni Source code
pml.nni.old Source code
pml.quartet Source code
pmlCluster Man page Source code
pmlCluster.fit Source code
pmlMix Man page Source code
pmlMixPen Source code
pmlPart Man page Source code
pmlPart2multiPhylo Man page Source code
pmlPartPen Source code
pmlPen Man page Source code
pnodes Source code
pnodesNew Source code
pratchet Man page Source code
prepareDataFitch Source code
prepareDataSankoff Source code
prepareDataSankoffNew Source code
presenceAbsence Man page Source code
presenceAbsenceOld Source code
print.SOWH Source code
print.phyDat Source code
print.pml Source code
print.pmlMix Source code
print.pmlPart Source code
print.splits Man page Source code
print.summary.clanistics Source code
prob2fitchCoding Source code
pruneTree Man page Source code
ptree Source code
rNNI Man page Source code
rNNI_old Source code
rSPR Man page Source code
rSPR_Old Source code
random.addition Man page Source code
read.FASTA.AA Source code
read.aa Man page Source code
read.nexus.networx Man page Source code
read.nexus.splits Man page Source code
read.phyDat Man page Source code
readAArate Source code
readDist Man page Source code
reduc Source code
removeNonsense Source code
removeParsUninfoSites Source code
removeTrivialSplits Man page Source code
removeUndeterminedSites Man page Source code
reorder.networx Source code
reorderPruning Source code
reroot Source code
reroot2 Source code
rnodes Source code
rooted.nni Source code
rowMin Source code
sankoff Man page Source code
sankoff.nni Source code
sankoff.quartet Source code
sankoffNew Source code
score Source code
seq2split Source code
shannon Source code
shannon2 Source code
simSeq Man page Source code
simSeq.phylo Man page Source code
simSeq.pml Man page Source code
split2seq Source code
splits Man page
splits2design Source code
splitsNetwork Man page Source code
sprMove Source code
sprdist Man page Source code
start_tree Source code
subsChoice Source code
subset.phyDat Man page Source code
summary.SOWH Source code
summary.clanistics Source code
superTree Man page Source code
threshStateC Man page Source code
treedist Man page Source code
unique.dist Man page Source code
unique.phyDat Man page Source code
unique.splits Man page Source code
update.pml Source code
update.pmlNew Source code
updateDM Source code
upgma Man page
upgma.edge.length Source code
upgma_nni Source code
upperBound Source code
vcov.pml Source code
wRF.dist Man page Source code
wRF0 Source code
wRF1 Source code
wRF2 Source code
wpgma Man page
write.nexus.dist Man page Source code
write.nexus.networx Man page Source code
write.nexus.splits Man page Source code
write.phyDat Man page Source code
write.phylip Source code
write.splits Man page Source code
writeDist Man page Source code
yeast Man page
zeroWise Source code
phangorn documentation built on Feb. 16, 2018, 1:02 a.m.