API for phangorn
Phylogenetic Reconstruction and Analysis

Global functions
.di2multi2di	Source code
.ratchet_fun	Source code
.stochastic_fun	Source code
.updateQBF	Source code
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
CodonQ	Source code
Descendants	Man page Source code
F1x4	Source code
F3x4	Source code
F3x4_freq	Source code
KF.dist	Man page Source code
Laguerre	Source code
LaguerreQuad	Source code
Laurasiatherian	Man page
NJ	Man page Source code
RF.dist	Man page Source code
RF0	Source code
RI	Man page Source code
Rx	Source code
SH.test	Man page Source code
SH.tmp	Source code
SH_quartet	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
Transfer_Index	Source code
UNJ	Man page Source code
[.phyDat	Man page
acctran	Man page Source code
acctran2	Source code
acgt2ry	Man page Source code
add.tips	Man page Source code
addConfidences	Man page Source code
addConfidences.multiPhylo	Source code
addConfidences.networx	Source code
addConfidences.phylo	Man page Source code
addConfidences.splits	Source code
addConfidencesMultiPhylo	Source code
addEdge	Source code
addOne	Source code
addOneTree	Source code
addTaxa	Source code
addTrivialSplits	Man page Source code
add_boxplot	Man page Source code
add_ci	Man page Source code
add_edge_length	Man page Source code
add_gap_Q_AA	Source code
add_gap_bf_AA	Source code
add_mutations	Man page Source code
add_support	Man page Source code
add_tiplabels	Source code
aic.weights	Source code
allAncestors	Source code
allChildren	Source code
allChildrenCPP	Source code
allCircularSplits	Man page Source code
allCompat	Man page Source code
allDescCPP	Source code
allDescendants	Man page Source code
allSiblingsCPP	Source code
allSitePattern	Man page Source code
allSplits	Man page Source code
allTrees	Man page Source code
anc_pars	Man page Source code
anc_pml	Man page Source code
ancestral.pars	Man page Source code
ancestral.pml	Man page Source code
ancstat	Source code
anova.pml	Man page Source code
as.AAbin.phyDat	Man page Source code
as.DNAbin.phyDat	Man page
as.Matrix	Man page Source code
as.Matrix.splits	Man page Source code
as.MultipleAlignment	Man page
as.MultipleAlignment.phyDat	Man page Source code
as.StringSet	Man page
as.StringSet.phyDat	Man page Source code
as.ancestral	Man page Source code
as.bitsplits.splits	Man page Source code
as.character.phyDat	Man page
as.data.frame.ancestral	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
as.phyDat.AAStringSet	Man page Source code
as.phyDat.AAbin	Man page Source code
as.phyDat.DNAStringSet	Man page Source code
as.phyDat.DNAbin	Man page Source code
as.phyDat.MultipleAlignment	Man page Source code
as.phyDat.alignment	Man page
as.phyDat.ancestral	Man page Source code
as.phyDat.character	Man page
as.phyDat.data.frame	Man page
as.phyDat.factor	Man page Source code
as.phyDat.matrix	Man page
as.phylo.splits	Man page Source code
as.pml	Man page
as.pml.modelTest	Source code
as.prop.part.splits	Man page Source code
as.splits	Man page Source code
as.splits.bitsplits	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
bf_by_codon	Source code
bip	Source code
bipCPP	Source code
bipart	Source code
bipartCPP	Source code
bootstrap.phyDat	Man page Source code
bootstrap.pml	Man page Source code
c.phyDat	Man page
c.splits	Man page Source code
candidate_tree	Man page Source code
cbind.phyDat	Man page Source code
changeEdge	Source code
changeEdgeLength	Source code
changeOrder	Source code
char2pos	Source code
checkLabels	Source code
check_tip_dates	Source code
chloroplast	Man page
circ.mean	Source code
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
codonTest	Man page Source code
comp	Source code
comp2	Source code
compareSplits	Source code
compatible	Man page Source code
compatible3	Source code
compatibleSplits	Source code
compatible_2	Source code
composition_test	Man page Source code
compress.phyDat	Source code
compressSites	Source code
consensusNet	Man page Source code
constSitePattern	Source code
const_site	Source code
coords	Man page Source code
coords.equal.angle	Source code
coph	Source code
cophenetic.networx	Man page Source code
cophenetic.splits	Man page Source code
cophenetic_cpp	Source code
countCycle2_cpp	Source code
countCycle_cpp	Source code
countCycles	Source code
count_mutations	Source code
createLabel	Man page Source code
dec2Bin	Source code
deg2rad	Source code
delta.quartet	Source code
delta.score	Man page Source code
densiTree	Man page Source code
descAll	Source code
designAll	Source code
designCalibrated	Source code
designConstrained	Source code
designSplits	Man page Source code
designStar	Source code
designTipDated	Source code
designTree	Man page Source code
designUltra	Source code
designUnrooted	Source code
designUnrooted2	Source code
df_freq_codon	Source code
dfactorial	Man page
discrete.beta	Man page Source code
discrete.gamma	Man page Source code
discrete.gamma.2	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
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
dna2aa	Man page Source code
dna2codon	Man page Source code
dropNode	Source code
dropTip	Source code
edQt	Man page Source code
edQt2	Source code
edgeLabels	Source code
edge_length_matrix	Source code
extract_prob	Source code
extract_states	Source code
fhm	Man page Source code
fhm_new	Source code
findRoots	Source code
fit.sankoff	Source code
fitch	Man page Source code
fitchCoding2ambiguous	Source code
fitch_nni	Source code
fn.quartet	Source code
fs	Source code
fun.rf	Source code
fun.spr	Source code
fun1	Source code
fun2	Source code
gap_as_ambiguous	Man page Source code
gap_as_state	Man page Source code
genlight2phyDat	Man page Source code
getAges	Source code
getClans	Man page
getClips	Man page
getDiv	Source code
getDiversity	Man page
getIndex	Source code
getModelAA	Source code
getOrder	Source code
getOrderingNN	Source code
getP	Source code
getRoot	Man page Source code
getScaler	Source code
getSlices	Man page Source code
getTransition	Source code
getdP	Source code
getdP2	Source code
glance	Man page
glance.phyDat	Man page
glance.pml	Source code
glance.pmlMix	Source code
grp_duplicated	Source code
guess_model	Source code
h2st	Man page Source code
h4st	Man page Source code
hadamard	Man page Source code
hasAmbiguousSites	Source code
has_gap_state	Man page Source code
hash	Man page
hash.multiPhylo	Source code
hash.phylo	Source code
highest_state	Source code
identical_sites	Source code
identify.networx	Man page Source code
ilb	Source code
image.phyDat	Man page Source code
index.nni	Source code
index2edge	Source code
index2tree	Source code
index2tree2	Source code
indexNNI	Source code
indexNNI3	Source code
indexNNI_fitch	Source code
init_fitch	Source code
init_rell	Source code
joint_pml	Source code
joint_sankoff	Source code
kSPR	Source code
kart2kreis	Source code
kart2kugel	Source code
keep_as_tip	Man page Source code
kf0	Source code
kf1	Source code
kf2	Source code
kreis2kart	Source code
kugel2kart	Source code
latag2n.phyDat	Man page Source code
ldfactorial	Man page Source code
lento	Man page Source code
lli	Man page Source code
logLik.pml	Man page Source code
logLik.pmlMix	Source code
logLik.pmlPart	Source code
logLik_pmlMix	Source code
lowerBound	Source code
mRF	Source code
mRF2	Source code
makeAncNodeLabel	Source code
makePart	Source code
map_duplicates	Man page Source code
map_mutations	Source code
mast	Man page Source code
mast.fit	Source code
matchSplits	Man page Source code
maxCladeCred	Man page Source code
mcc	Man page
midpoint	Man page Source code
midpoint.multiPhylo	Man page Source code
midpoint.phylo	Man page Source code
minEdge	Source code
mites	Man page
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
neb	Source code
neighborNet	Man page Source code
networx	Man page
new2old.phyDat	Source code
nni	Man page Source code
nni2	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
node_height_cpp	Source code
old2new.phyDat	Source code
oneOf4	Source code
optEdgeMulti	Source code
optNNI	Source code
optW	Source code
optWPen	Source code
opt_Edge	Source code
opt_nni	Source code
optim.fitch	Source code
optim.parsimony	Man page Source code
optim.pml	Man page Source code
optim.quartet	Source code
optim.sankoff	Source code
optimAllRate	Source code
optimBf	Source code
optimCodon	Source code
optimEdge	Source code
optimF3x4	Source code
optimFreeRate	Source code
optimGamma	Source code
optimInv	Source code
optimMixBf	Source code
optimMixEdge	Source code
optimMixInv	Source code
optimMixM1a	Source code
optimMixM2a	Source code
optimMixM7	Source code
optimMixQ	Source code
optimMixRate	Source code
optimMixTSTV	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
optimWs	Source code
orderNNI	Source code
out_cpp	Source code
p2dna	Source code
pace	Man page
parsimony	Man page 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
phyDat2MultipleAlignment	Man page
phyDat2alignment	Man page Source code
plot.codonTest	Source code
plot.networx	Man page Source code
plot.pml	Man page 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
plotRates	Man page Source code
plotSeqLogo	Man page Source code
plot_gamma_plus_inv	Man page 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.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
pml_bb	Man page Source code
pnodes	Source code
pnodes2	Source code
pratchet	Man page Source code
prepareDataSankoff	Source code
presenceAbsence	Man page Source code
print.SOWH	Source code
print.ancestral	Man page Source code
print.codonTest	Source code
print.phyDat	Man page
print.pml	Man page Source code
print.pmlMix	Source code
print.pmlPart	Source code
print.splits	Man page Source code
print.summary.clanistics	Source code
proper_tree	Source code
pruneTree	Man page Source code
ptree	Source code
rNNI	Man page Source code
rSPR	Man page Source code
rad2deg	Source code
random.addition	Man page
ratchet.control	Man page Source code
rates_n_weights	Source code
rbind.phyDat	Source code
read.nexus.charset	Source code
read.nexus.dist	Man page Source code
read.nexus.networx	Man page Source code
read.nexus.partitions	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
readPhylip	Source code
reduc	Source code
reexports	Man page
relabel	Source code
removeAmbiguousSites	Man page Source code
removeParsUninfoSites	Source code
removeParsimonyUninfomativeSites	Source code
removeTrivialSplits	Man page Source code
removeUndeterminedSites	Man page Source code
remove_similar	Source code
reorder.networx	Source code
rnodes	Source code
rooted.nni	Source code
rotate_matrix	Source code
sankoff	Man page Source code
sankoff_nni	Source code
score	Source code
seq2split	Source code
seq_stats	Source code
short_bipCPP	Source code
simSeq	Man page Source code
simSeq.phylo	Man page Source code
simSeq.pml	Man page Source code
sorted_bipartCPP	Source code
spl2angle	Source code
split2seq	Source code
split_model	Source code
splits	Man page
splits2design	Source code
splits2phylo	Source code
splitsNetwork	Man page Source code
sprdist	Man page Source code
subsChoice	Source code
subsChoice_USER	Source code
subset.phyDat	Man page
summary.SOWH	Source code
summary.clanistics	Man page Source code
superTree	Man page Source code
supgma	Man page Source code
support	Source code
synonymous_subs	Source code
threshStateC	Man page Source code
tidy	Man page
tidy.modelTest	Source code
transferBootstrap	Man page Source code
tree2phyDat	Source code
treedist	Man page Source code
tstv_subs	Source code
uncompress.phyDat	Source code
unique.dist	Man page Source code
unique.phyDat	Man page Source code
unique.splits	Man page Source code
update.pml	Source code
updateDM	Source code
updateRates	Source code
update_rell	Source code
upgma	Man page Source code
upperBound	Source code
vcov.pml	Man page Source code
wRF.dist	Man page Source code
wRF0	Source code
wRF1	Source code
wRF2	Source code
wpgma	Man page Source code
write.ancestral	Man page Source code
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.pml	Man page Source code
write.splits	Man page Source code
writeDist	Man page Source code
yeast	Man page