Index

A | B | C | D | E | F | G | H | I | L | M | N | O | P | Q | R | S | T | U | V | W | X

A

addLeaf() (Tree method)
addLeafToBigT() (QuartetJoining method)
addNodeBetweenNodes() (Tree method)
addSibLeaf() (Tree method)
addSubTree() (Tree method)
addUnusedTaxaIfTheyHaveThreeKBrs() (QuartetJoining method)
addXSubTreeToBigT() (QuartetJoining method)
Alignment (class in p4.alignment)
alignment() (SequenceList method)
alignments (Var attribute)
allBiRootedTrees() (Tree method)
allChooseFour() (QuartetJoining method)
andMasks() (Alignment method)
argvAfterDoubleDash (Var attribute)
arithmeticMeanOfLogs() (Numbers method)
autoTune() (Mcmc method)

B

bigXSquaredSubM() (Tree method)
binSize (Numbers attribute)
bionj() (DistanceMatrix method)
bluntEndLigate() (Alignment method)
bootstrap() (Alignment method)
(Data method)
breakTie() (QuartetJoining method)
btv() (Tree method)
buildDecoratedTree() (SuperTreeSupport method)

C

calcLogLike() (Tree method)
calculateBitKeyForInternalNodeFromChildren() (QuartetJoining method)
calcUnconstrainedLogLikelihood1() (Data method)
calcUnconstrainedLogLikelihood2() (Data method)
changeDataTypeTo() (Alignment method)
charsets() (in module p4.func)
checkBigTInternalNodes() (QuartetJoining method)
checkBitKeys() (QuartetJoining method)
checkDupedTaxonNames() (Tree method)
checkForAllGapColumns() (Alignment method)
checkForBlankSequences() (Alignment method)
checkForDuplicateSequences() (Alignment method)
checkLengthsAndTypes() (Alignment method)
checkNamesForDupes() (SequenceList method)
checkPoint() (STMcmc method)
checkSplitKeys() (Tree method)
checkTaxNames() (Tree method)
(Trees method)
checkThatAllSelfNodesAreInTheTree() (Tree method)
checkTranslation() (Alignment method)
chiSquaredProb() (in module p4.func)
clustalo() (SequenceList method)
collapseNode() (Tree method)
collapseNodesAndAddUnusedTaxa() (QuartetJoining method)
combineWith() (TreePartitions method)
compareSplits() (McmcCheckPointReader method)
(TreePartitions method)
compareSplitsAll() (McmcCheckPointReader method)
compareSplitsBetweenTwoTreePartitions() (McmcCheckPointReader static method)
compoChiSquaredTest() (Data method)
composition() (Alignment method)
compositionEuclideanDistanceMatrix() (Alignment method)
compoSummary() (Data method)
compoTestUsingSimulations() (Tree method)
compStatFromCharFreqs() (Tree method)
concatenate() (Alignment method)
consel() (Trees method)
consensus() (TreePartitions method)
constantMask() (Alignment method)
constantSitesCount() (Alignment method)
constantSitesProportion() (Alignment method)
Constraints (class in p4.constraints)
copyToTree() (Tree method)
covarionStats() (Alignment method)

D

Data (class in p4.data)
data (Tree attribute)
dataType (Alignment attribute)
decorateTreeWithBitKeys() (QuartetJoining method)
deleteCStuff() (Tree method)
dim (Alignment attribute)
dirichlet1() (in module p4.func)
dirichlet2() (in module p4.func)
DistanceMatrix (class in p4.distancematrix)
doSplash (Var attribute)
draw() (Tree method)
dump() (Alignment method)
(Constraints method)
(Data method)
(McmcCheckPointReader method)
(Model method)
(NexusSets method)
(Numbers method)
(QuartetJoining method)
(Sequence method)
(SequenceList method)
(Tree method)
(TreePartitions method)
(Trees method)
(in module p4.func)
dupe() (Alignment method)
(Data method)
(Sequence method)
(Tree method)
dupeCharSet() (NexusSets method)
dupeSubTree() (Tree method)

E

effectiveSampleSize() (in module p4.func)
eps() (Tree method)
equates (Alignment attribute)
examplesDir (Var attribute)
excepthookEditor (Var attribute)
excludeCharSet() (Alignment method)

F

factorial() (in module p4.func)
fastme() (DistanceMatrix method)
fileNames (Var attribute)
fixCharsForLatex() (in module p4.func)
fName (SequenceList attribute)

G

gappedMask() (Alignment method)
GeneticCode (class in p4.geneticcode)
getAllGapsMask() (Alignment method)
getAllLeafNames() (Tree method)
getAnInputTreeForTheStartingTree() (QuartetJoining method)
getBigQ() (Model method)
getCharDiversityDistribution() (Alignment method)
getChildrenNums() (Tree method)
getDegree() (Tree method)
getEnoughCharsMask() (Alignment method)
getEuclideanDistanceFromSelfDataToExpectedComposition() (Tree method)
getKNodes() (QuartetJoining method)
getKosiolAISGroups() (Alignment method)
getLen() (Tree method)
getLikelihoodTopologyInformativeSitesMask() (Alignment method)
getMaskForAutapomorphies() (Alignment method)
getMaskForCharDiversity() (Alignment method)
getMinmaxChiSqGroups() (Alignment method)
getNChildren() (Node method)
getNodeNumsAbove() (Tree method)
getPreAndPostOrderAbove() (Tree method)
getPreAndPostOrderAboveRoot() (Tree method)
getQuartetForFourTaxaInTrees() (QuartetJoining method)
getQuartetsForXForNode() (QuartetJoining method)
getSample() (PosteriorSamples method)
getSeqNumsAbove() (Tree method)
getSimpleBigF() (Alignment method)
getSiteLikes() (Tree method)
getSiteRates() (Tree method)
getSplitForTaxNames() (TreePartitions method)
getSplitKeyFromTaxNames() (in module p4.func)
getSplitStringFromKey() (in module p4.func)
getStartingTreeFromQuartet() (QuartetJoining method)
getStartingTreeFromQuartet_highFrequencyFirst() (QuartetJoining method)
getStartingTreeFromQuartet_randomTaxa() (QuartetJoining method)
getTaxBitsString() (QuartetJoining method)
getTree() (TreeFileLite method)
getTreesWithSplit() (Trees method)
getWeightCommandComment() (Tree method)
gsl_meanVariance() (in module p4.func)
(Numbers method)
gsl_ran_dirichlet() (in module p4.func)
gsl_ran_gamma() (in module p4.func)

H

harmonicMeanOfLogs() (Numbers method)
hasGapsOrAmbiguities() (Alignment method)
histo() (Numbers method)

I

initDataParts() (Alignment method)
inputTreesToSuperTreeDistances() (Tree method)
(Trees method)
interactiveHelper (Var attribute)
isAncestorOf() (Node method)
isDnaRnaOrProtein() (in module p4.func)
isFullyBifurcating() (Tree method)
iterChildren() (Node method)
iterDown() (Node method)
iterInternals() (Node method)
(Tree method)
iterInternalsNoRoot() (Tree method)
iterInternalsNoRootPostOrder() (Tree method)
iterInternalsNoRootPreOrder() (Tree method)
iterInternalsPostOrder() (Tree method)
iterLeaves() (Node method)
iterLeavesNoRoot() (Tree method)
iterLeavesPostOrder() (Tree method)
iterLeavesPreOrder() (Tree method)
iterNodes() (Tree method)
iterNodesNoRoot() (Tree method)
iterPostOrder() (Node method)
(Tree method)
iterPreOrder() (Node method)
(Tree method)

L

ladderize() (Tree method)
leftSibling() (Node method)
lineUpLeaves() (Tree method)
listOfSplits() (Reduced method)
locateAndCountLeavesInXSubTreeFromQuartet() (QuartetJoining method)
logDet() (Alignment method)
ls() (in module p4.func)

M

majorityRuleConsensus() (Reduced method)
makeSequenceForNameDict() (SequenceList method)
makeSplitKeys() (Tree method)
makeStartingQuartetFromAllTrees() (QuartetJoining method)
makeTreeFromPartitions() (TreePartitions method)
maskFromNexusCharacterList() (in module p4.func)
matchedPairsTests() (Alignment method)
Mcmc (class in p4.mcmc)
McmcCheckPointReader (class in p4.mcmccheckpointreader)
mean() (in module p4.func)
(Numbers method)
meanNCharsPerSite() (Alignment method)
(Data method)
Model (class in p4.model)
model (Tree attribute)
modelFitTests() (Tree method)
modelSanityCheck() (Tree method)
modelSymbols (Var attribute)
mrp() (in module p4.mrp)
mrpSlice() (Alignment method)
muscle() (SequenceList method)

N

nChar (Alignment attribute)
(Sequence attribute)
nChooseK() (in module p4.func)
nEquates (Alignment attribute)
newCharSet() (NexusSets method)
newComp() (Tree method)
newEmptyAlignment() (in module p4.func)
newGdasrv() (Tree method)
newick_allowSpacesInNames (Var attribute)
newRMatrix() (Tree method)
newtonRaftery94_eqn16() (in module p4.func)
nextNode() (Tree method)
nexus_allowAllDigitNames (Var attribute)
nexus_allowUTREE (Var attribute)
nexus_getAllCommandComments (Var attribute)
nexus_getLineEndingsAsTokens (Var attribute)
nexus_getP4CommandComments (Var attribute)
nexus_getWeightCommandComments (Var attribute)
nexus_ignoreFormatCommandSymbols (Var attribute)
nexus_readBeastTreeCommandComments (Var attribute)
nexus_warnSkipUnknownBlock (Var attribute)
nexus_warnSwitchGapChar (Var attribute)
nexus_warnSwitchMissingChar (Var attribute)
nexus_writeVisibleComments (Var attribute)
nexusCheckName() (in module p4.func)
nexusFixNameIfQuotesAreNeeded() (in module p4.func)
nexusSets (Alignment attribute)
NexusSets (class in p4.nexussets)
nexusSets (Var attribute)
nexusUnquoteAndDeUnderscoreName() (in module p4.func)
nexusUnquoteName() (in module p4.func)
nInternalNodes (Tree attribute)
njUsingPaup() (DistanceMatrix method)
nni() (Tree method)
Node (class in p4.node)
node() (Tree method)
noGapsOrAmbiguitiesCopy() (Alignment method)
nRootedTrees() (in module p4.func)
nRootedTreesWithMultifurcations() (in module p4.func)
nTax (Alignment attribute)
(QuartetJoining attribute)
(Tree attribute)
(Trees attribute)
nTrees (QuartetJoining attribute)
Numbers (class in p4.pnumbers)
nUnrootedTrees() (in module p4.func)
nUnrootedTreesWithMultifurcations() (in module p4.func)

O

optLogLike() (Tree method)
optTest() (Tree method)
orMasks() (Alignment method)

P

p4.alignment (module)
p4.constraints (module)
p4.data (module)
p4.distancematrix (module)
p4.func (module)
p4.geneticcode (module)
p4.mcmc (module)
p4.mcmccheckpointreader (module)
p4.model (module)
p4.mrp (module)
p4.nexussets (module)
p4.node (module)
p4.pnumbers (module)
p4.posteriorsamples (module)
p4.quartetjoining (module)
p4.reducedstrictconsensus (module)
p4.sequencelist (module), [1]
p4.stmcmc (module)
p4.supertreesupport (module)
p4.tree (module)
p4.treefilelite (module)
p4.treepartitions (module)
p4.trees (module)
p4.var (module)
parseNewick() (Tree method)
parseNexus() (Tree method)
parts (Alignment attribute)
patristicDistanceMatrix() (Tree method)
pause() (QuartetJoining method)
pDistances() (Alignment method)
phylipDataMaxNameLength (Var attribute)
plot() (Numbers method)
polar2square() (in module p4.func)
popcount() (QuartetJoining method)
(SuperTreeSupport method)
popcountLimit() (SuperTreeSupport method)
PosteriorSamples (class in p4.posteriorsamples)
printReducedOutput() (SuperTreeSupport method)
printSplitList() (SuperTreeSupport method)
pruneSubTreeWithoutParent() (Tree method)
putGaps() (Alignment method)

Q

QuartetJoining (class in p4.quartetjoining)
quartetJoining() (QuartetJoining method)

R

randomizeTopology() (Tree method)
randomSpr() (Tree method)
randomTree() (in module p4.func)
read() (in module p4.func)
(Numbers method)
(TreePartitions method)
readAndPop() (in module p4.func)
readBipartitionsFromPaupLogFile() (Tree method)
readFile() (in module p4.func)
readOpenPhylipFile() (Alignment method)
readPhylipFile() (DistanceMatrix method)
recalculateSplitKeysOfNodeFromChildren() (Tree method)
recipes() (in module p4.func)
recodeDayhoff() (Alignment method)
recodeProteinIntoGroups() (Alignment method)
recodeRY() (Alignment method)
reconnectSubTreeWithoutParent() (Tree method)
Reduced (class in p4.reducedstrictconsensus)
reducedConsensusProfile() (Reduced method)
reducedMemQuick() (Reduced method)
reducedQuick() (Reduced method)
reducedStrictConsensus() (Reduced method)
refineKSubTree() (QuartetJoining method)
rell() (Trees method)
removeAboveNode() (Tree method)
removeEverythingExceptCladeAtNode() (Tree method)
removeNode() (Tree method)
removeRoot() (Tree method)
renameForPhylip() (SequenceList method)
(Tree method)
reRoot() (Tree method)
reseedCRandomizer() (in module p4.func)
resetPartsContentFromSequences() (Alignment method)
resetSequencesFromParts() (Alignment method)
(Data method)
restoreDupeTaxa() (Tree method)
restoreNamesFromRenameForPhylip() (SequenceList method)
(Tree method)
reverseComplement() (Sequence method)
reverseMrp() (in module p4.mrp)
rightmostChild() (Node method)
rMatrixNormalizeTo1 (Var attribute)
rMatrixProteinSpecs (Var attribute)
rotateAround() (Tree method)
run() (Mcmc method)
(STMcmc method)

S

saveIndexTree() (SuperTreeSupport method)
Sequence (class in p4.sequencelist)
sequenceForNameDict (SequenceList attribute)
SequenceList (class in p4.sequencelist)
sequenceLists (Var attribute)
sequences (SequenceList attribute)
sequenceSlice() (Alignment method)
setCharPartition() (Alignment method)
setCStuff() (Tree method)
setDim() (DistanceMatrix method)
setEmpiricalComps() (Tree method)
setGBlocksCharSet() (Alignment method)
setModelThing() (Tree method)
setModelThingsNNodes() (Tree method)
setModelThingsRandomly() (Tree method)
setNexusSets() (Alignment method)
(Tree method)
setNGammaCat() (Tree method)
setPInvar() (Tree method)
setPreAndPostOrder() (Tree method)
setRelRate() (Tree method)
setRjComp() (Tree method)
setRjRMatrix() (Tree method)
setTaxNames() (Trees method)
setTerminalColor() (in module p4.func)
setTerminalColour() (in module p4.func)
setTextDrawSymbol() (Tree method)
setTreeTaxBits() (QuartetJoining method)
simpleBigXSquared() (Data method)
simpleCharCounts() (Alignment method)
simpleConstantMask() (Alignment method)
simpleConstantSitesCount() (Data method)
simsForModelFitTests() (Tree method)
simulate() (Tree method)
sortListOfListsOnListElementNumber() (in module p4.func)
sortListOfObjectsOn2Attributes() (in module p4.func)
sortListOfObjectsOnAttribute() (in module p4.func)
spaceDelimitedToTabDelimited() (in module p4.func)
splash() (in module p4.func)
spr() (Tree method)
square2polar() (in module p4.func)
STMcmc (class in p4.stmcmc)
strictRunNumberChecking (Var attribute)
stringZapWhitespaceAndDigits() (in module p4.func)
stripBrLens() (Tree method)
studentsTStat() (in module p4.func)
studentsTTest1() (in module p4.func)
subsetUsingCharSet() (Alignment method)
subsetUsingMask() (Alignment method)
subTreeIsFullyBifurcating() (Tree method)
summarizeMcmcPrams() (in module p4.func)
summarizeModelThingsNNodes() (Tree method)
summarizeUnusedTaxa() (QuartetJoining method)
SuperTreeSupport (class in p4.supertreesupport)
superTreeSupport() (SuperTreeSupport method)
symbols (Alignment attribute)

T

tailAreaProbability() (in module p4.func)
(Numbers method)
taxNames (Alignment attribute)
(Tree attribute)
taxSetIsASplit() (Tree method)
testOverallFromAbabnehEtAl2006() (Alignment method)
textDrawList() (Tree method)
topologyDistance() (Tree method)
topologyDistanceMatrix() (Trees method)
topologyDistanceMetrics (Var attribute)
tPickle() (Tree method)
trackSplitsFromTree() (Trees method)
translate() (Alignment method)
(GeneticCode method)
(Sequence method)
Tree (class in p4.tree)
TreeFileLite (class in p4.treefilelite)
TreePartitions (class in p4.treepartitions)
treeProbabilities() (Trees method)
Trees (class in p4.trees)
trees (Var attribute)
tryToAddAnyX() (QuartetJoining method)
tryToAddAParticularX() (QuartetJoining method)
tv() (Tree method)
tvTopologyCompare() (Tree method)

U

uninstall() (in module p4.func)
uniqueFile() (in module p4.func)
unPickleMcmc() (in module p4.func)
unPickleSTMcmc() (in module p4.func)
unsetTerminalColor() (in module p4.func)
unsetTerminalColour() (in module p4.func)

V

Var (class in p4.var)
variance() (in module p4.func)
verboseRead (Var attribute)
verifyIdentityWith() (Tree method)

W

warnReadNoFile (Var attribute)
which() (in module p4.func)
which2() (in module p4.func)
wipe() (Node method)
wise2Table() (GeneticCode method)
write() (NexusSets method)
(Sequence method)
(Tree method)
writeExtended() (Reduced method)
writeFasta() (Sequence method)
(SequenceList method)
writeFastaToOpenFile() (Sequence method)
writeFastaUppercase (Var attribute)
writeInColor() (in module p4.func)
writeInColour() (in module p4.func)
writeIntersections() (Reduced method)
writeMolphy() (Alignment method)
writeNewick() (Tree method)
(Trees method)
writeNexus() (Alignment method)
(Data method)
(DistanceMatrix method)
(NexusSets method)
(Tree method)
(Trees method)
writeNexusToOpenFile() (DistanceMatrix method)
(NexusSets method)
writePhylip() (Alignment method)
(DistanceMatrix method)
(Tree method)
writePhylipToOpenFile() (DistanceMatrix method)
writeProposalAcceptances() (Mcmc method)
(McmcCheckPointReader method)
(STMcmc method)
writeProposalIntendedProbs() (Mcmc method)
(STMcmc method)
writeProposalProbs() (Mcmc method)
(McmcCheckPointReader method)
(STMcmc method)
writeSplits() (TreePartitions method)
writeSwapMatrices() (McmcCheckPointReader method)
writeSwapMatrix() (Mcmc method)
(STMcmc method)

X

xSquared() (in module p4.func)