Index

_

__init__() (pylogeny.alignment.alignment method) (pylogeny.JSONWriter.JSONWriter method) (pylogeny.alignment.phylipFriendlyAlignment method) (pylogeny.base.treeBranch method) (pylogeny.base.treeNode method) (pylogeny.base.treeStructure method) (pylogeny.base.trie method) (pylogeny.database.SQLDatabase method) (pylogeny.database.SQLExhaustiveLandscape method) (pylogeny.database.SQLiteDatabase method) (pylogeny.database.SQLiteLandscape method) (pylogeny.database.database method) (pylogeny.executable.aTemporaryDirectory method) (pylogeny.executable.consel method) (pylogeny.executable.fasttree method) (pylogeny.executable.raxml method) (pylogeny.executable.rspr method) (pylogeny.executable.treepuzzle method) (pylogeny.heuristic.RAxMLIdentify method) (pylogeny.heuristic.heuristic method) (pylogeny.heuristic.likelihoodGreedy method) (pylogeny.heuristic.parsimonyGreedy method) (pylogeny.heuristic.phylogeneticLinearHeuristic method) (pylogeny.heuristic.smoothGreedy method) (pylogeny.landscape.graph method) (pylogeny.landscape.landscape method) (pylogeny.landscape.vertex method) (pylogeny.landscapeWriter.landscapeParser method) (pylogeny.landscapeWriter.landscapeWriter method) (pylogeny.model.DiscreteStateModel method) (pylogeny.model.PhyloModelError method) (pylogeny.newick.ParsingError method) (pylogeny.newick.branch method) (pylogeny.newick.newickParser method) (pylogeny.newick.node method) (pylogeny.parsimony.profile_set method) (pylogeny.parsimony.site_profile method) (pylogeny.pll.dataModel method) (pylogeny.pll.partitionModel method) (pylogeny.rearrangement.RearrangementError method) (pylogeny.rearrangement.rearrangement method) (pylogeny.rearrangement.topology method) (pylogeny.tree.bipartition method) (pylogeny.tree.tree method) (pylogeny.tree.treeSet method)

A

addChild() (pylogeny.base.treeNode method) addTree() (pylogeny.landscape.landscape method) (pylogeny.tree.treeSet method) addTreeByNewick() (pylogeny.landscape.landscape method) (pylogeny.tree.treeSet method) alignment (class in pylogeny.alignment) allNNI() (pylogeny.rearrangement.topology method) allNNIForBranch() (pylogeny.rearrangement.topology method)

allSPR() (pylogeny.rearrangement.topology method) allSPRForBranch() (pylogeny.rearrangement.topology method) allType() (pylogeny.rearrangement.topology method) approximatePossibleNumNeighbors() (pylogeny.landscape.vertex method) assignParents() (in module pylogeny.newick) aTemporaryDirectory (class in pylogeny.executable)

B

beaglegetLogLikelihood() (in module pylogeny.scoring) bestTree (pylogeny.heuristic.phylogeneticLinearHeuristic attribute)

bipartition (class in pylogeny.tree) branch (class in pylogeny.newick)

C

clearEdgeWeights() (pylogeny.landscape.graph method) close() (pylogeny.alignment.alignment method) (pylogeny.database.SQLDatabase method) (pylogeny.database.SQLiteDatabase method) (pylogeny.database.database method) (pylogeny.pll.dataModel method) (pylogeny.pll.partitionModel method) connect() (pylogeny.database.SQLDatabase method) consel (class in pylogeny.executable)

convertOriginalNewick() (pylogeny.alignment.phylipFriendlyAlignment method) createModel() (pylogeny.pll.partitionModel method) createSimpleModel() (pylogeny.pll.partitionModel method)

D

database (class in pylogeny.database) DatabaseLandscape (class in pylogeny.database) dataModel (class in pylogeny.pll) delete() (pylogeny.base.patriciaTree method) (pylogeny.base.trie method)

DiscreteStateModel (class in pylogeny.model) doMove() (pylogeny.rearrangement.rearrangement method) dup() (in module pylogeny.rearrangement)

E

executable (class in pylogeny.executable) exeExists() (in module pylogeny.executable) exeName (pylogeny.executable.executable attribute) (pylogeny.executable.fasttree attribute) (pylogeny.executable.raxml attribute) (pylogeny.executable.rspr attribute) (pylogeny.executable.treepuzzle attribute)

explore() (pylogeny.heuristic.heuristic method) (pylogeny.heuristic.RAxMLIdentify method) (pylogeny.heuristic.likelihoodGreedy method) (pylogeny.heuristic.parsimonyGreedy method) (pylogeny.heuristic.smoothGreedy method) exploreRandomTree() (pylogeny.database.SQLExhaustiveLandscape method) (pylogeny.landscape.landscape method) exploreTree() (pylogeny.database.SQLExhaustiveLandscape method) (pylogeny.landscape.landscape method)

F

fasttree (class in pylogeny.executable) filterRecords() (pylogeny.database.database method) findTree() (pylogeny.landscape.landscape method) findTreeTopology() (pylogeny.landscape.landscape method) findTreeTopologyByStructure() (pylogeny.landscape.landscape method)

fitch() (in module pylogeny.parsimony) fitch_cost() (in module pylogeny.parsimony) fromNewick() (pylogeny.rearrangement.topology method) fromStringRepresentation() (pylogeny.tree.bipartition method) fromTreeFile() (pylogeny.tree.treeSet static method)

G

get() (pylogeny.parsimony.profile_set method) getAlignment() (pylogeny.landscape.landscape method) (pylogeny.model.DiscreteStateModel method) getAlignmentAsStateList() (pylogeny.model.DiscreteStateModel method) getAllBranches() (in module pylogeny.newick) getAllLeaves() (pylogeny.base.treeStructure method) getAllNodes() (pylogeny.base.treeStructure method) getAllPathsOfBestImprovement() (pylogeny.landscape.landscape method) getAlphabet() (pylogeny.base.trie method) getApproxMLNewick() (pylogeny.alignment.alignment method) getApproxMLTree() (pylogeny.alignment.alignment method) getBalancingBracket() (in module pylogeny.newick) getBestImprovement() (pylogeny.landscape.landscape method) (pylogeny.landscape.vertex method) getBestSPRScore() (pylogeny.tree.bipartition method) getBestTree() (pylogeny.heuristic.phylogeneticLinearHeuristic method) getBipartitionFoundInTreeByIndex() (pylogeny.landscape.landscape method) getBipartitions() (pylogeny.landscape.vertex method) (pylogeny.rearrangement.topology method) getBipartitionScores() (pylogeny.landscape.vertex method) getBranch() (pylogeny.tree.bipartition method) getBranches() (pylogeny.rearrangement.topology method) getBranchFromBipartition() (pylogeny.rearrangement.topology method) getBranchFromStrBipartition() (pylogeny.rearrangement.topology method) getBranchIndex() (pylogeny.tree.bipartition method) getBranchLength() (in module pylogeny.newick) getBranchListRepresentation() (pylogeny.tree.bipartition method) getCenter() (pylogeny.landscape.graph method) getCharType() (pylogeny.model.DiscreteStateModel method) getChild() (pylogeny.base.treeBranch method) getChildByIndex() (pylogeny.base.treeNode method) getChildren() (pylogeny.base.treeNode method) getCliqueNumber() (pylogeny.landscape.graph method) getCliques() (pylogeny.landscape.graph method) getCliquesOfNode() (pylogeny.landscape.graph method) getColumns() (pylogeny.database.database method) (pylogeny.database.SQLDatabase method) (pylogeny.database.SQLiteDatabase method) getCompleteLandscape() (pylogeny.JSONWriter.JSONWriter method) getComponentOfNode() (pylogeny.landscape.graph method) getComponents() (pylogeny.landscape.graph method) getDatabaseNode() (pylogeny.database.SQLExhaustiveLandscape method) getDataType() (pylogeny.alignment.alignment method) getDegree() (pylogeny.landscape.vertex method) getDegreeFor() (pylogeny.landscape.graph method) getDiameter() (pylogeny.landscape.graph method) getDict() (pylogeny.landscape.vertex method) getDim() (pylogeny.alignment.alignment method) getEdge() (pylogeny.landscape.graph method) getEdges() (pylogeny.landscape.graph method) getEdgesFor() (pylogeny.landscape.graph method) getFASTA() (pylogeny.alignment.alignment method) getFileName() (pylogeny.pll.partitionModel method) getForTaxa() (pylogeny.parsimony.profile_set method) getFrequencyOfState() (pylogeny.model.DiscreteStateModel method) getGlobalOptimum() (pylogeny.landscape.landscape method) getHeaders() (pylogeny.database.database method) getIndex() (pylogeny.landscape.vertex method) getInstructionString() (pylogeny.executable.consel method) (pylogeny.executable.executable method) (pylogeny.executable.fasttree method) (pylogeny.executable.raxml method) (pylogeny.executable.rspr method) (pylogeny.executable.treepuzzle method) getInterval() (pylogeny.executable.consel method) getJSON() (pylogeny.JSONWriter.JSONWriter method) getLabel() (pylogeny.base.treeBranch method) (pylogeny.base.treeNode method) getLeafName() (in module pylogeny.newick) getLeaves() (pylogeny.rearrangement.topology method) getLocalOptima() (pylogeny.landscape.landscape method) getLocks() (pylogeny.landscape.landscape method) getLogLikelihood() (in module pylogeny.scoring) (pylogeny.pll.dataModel method) getMedianSPRScore() (pylogeny.tree.bipartition method) getMST() (pylogeny.landscape.graph method) getName() (pylogeny.landscapeWriter.landscapeParser method) (pylogeny.tree.tree method) getNeighbors() (pylogeny.landscape.vertex method) getNeighborsFor() (pylogeny.landscape.graph method) getNeighborsOfBipartition() (pylogeny.landscape.vertex method)

getNeighborsOfBranch() (pylogeny.landscape.vertex method) getNewick() (pylogeny.landscape.vertex method) (pylogeny.tree.tree method) getNewickString() (pylogeny.pll.dataModel method) getNode() (pylogeny.database.DatabaseLandscape method) (pylogeny.landscape.graph method) getNodeNames() (pylogeny.landscape.graph method) getNodes() (pylogeny.landscape.graph method) getNonEmptyChildrenBranches() (pylogeny.base.trieNode method) getNonEmptyChildrenBranchLabels() (pylogeny.base.trieNode method) getNonEmptyChildrenNodes() (pylogeny.base.trieNode method) getNumberTaxa() (pylogeny.landscape.landscape method) getNumCliques() (pylogeny.landscape.graph method) getNumComponents() (pylogeny.landscape.graph method) getNumSeqs() (pylogeny.alignment.alignment method) getObject() (pylogeny.landscape.vertex method) getOnlyImprovements() (pylogeny.JSONWriter.JSONWriter method) getOrigin() (pylogeny.landscape.vertex method) (pylogeny.tree.tree method) getParent() (pylogeny.base.treeBranch method) (pylogeny.base.treeNode method) getParentNode() (pylogeny.base.trieNode method) getParsimony() (in module pylogeny.scoring) getParsimonyForTopology() (in module pylogeny.scoring) getParsimonyFromProfiles() (in module pylogeny.scoring) getParsimonyFromProfilesForTopology() (in module pylogeny.scoring) getPath() (pylogeny.heuristic.phylogeneticLinearHeuristic method) getPathOfBestImprovement() (pylogeny.landscape.landscape method) (pylogeny.landscape.vertex method) getPhylip() (pylogeny.alignment.phylipFriendlyAlignment method) getPossibleNumberRootedTrees() (pylogeny.landscape.landscape method) getPossibleNumberUnrootedTrees() (pylogeny.landscape.landscape method) getPostOrderTraversal() (pylogeny.base.treeStructure method) getProperName() (pylogeny.alignment.phylipFriendlyAlignment method) getProperNewick() (pylogeny.landscape.vertex method) getRawFrequencyOfState() (pylogeny.model.DiscreteStateModel method) getRawStateFreqs() (pylogeny.model.DiscreteStateModel method) getRawStateFreqsAsDict() (pylogeny.model.DiscreteStateModel method) getRawStateFreqsAsList() (pylogeny.model.DiscreteStateModel method) getRecords() (pylogeny.database.database method) getRecordsAsDict() (pylogeny.database.database method) getRecordsColumn() (pylogeny.database.database method) getRejected() (pylogeny.executable.consel method) getRerootedNoBranchLengthNewick() (pylogeny.tree.tree method) getRoot() (pylogeny.base.treeStructure method) (pylogeny.base.trie method) (pylogeny.landscape.landscape method) getRootNode() (pylogeny.landscape.landscape method) getRootTree() (pylogeny.landscape.landscape method) getScore() (pylogeny.landscape.vertex method) (pylogeny.tree.tree method) getSequenceMatrix() (pylogeny.model.DiscreteStateModel method) getSequenceString() (pylogeny.alignment.alignment method) getShortestPath() (pylogeny.landscape.graph method) getShortestPathLength() (pylogeny.landscape.graph method) getShortStringMappings() (pylogeny.tree.bipartition method) getShortStringRepresentation() (pylogeny.tree.bipartition method) getSimpleNewick() (pylogeny.tree.tree method) getSiteLikelihoodFile() (pylogeny.executable.treepuzzle method) getSize() (pylogeny.alignment.alignment method) (pylogeny.landscape.graph method) getSPRDistance() (pylogeny.executable.rspr method) getSPRRearrangements() (pylogeny.tree.bipartition method) getSPRScores() (pylogeny.tree.bipartition method) getStartState() (pylogeny.heuristic.heuristic method) getStateFreqs() (pylogeny.model.DiscreteStateModel method) getStateGraph() (pylogeny.heuristic.heuristic method) getStateModel() (pylogeny.alignment.alignment method) getStrBipartitionFromBranch() (pylogeny.rearrangement.topology method) getStringRepresentation() (pylogeny.tree.bipartition method) getStructure() (pylogeny.tree.tree method) getTables() (pylogeny.database.database method) (pylogeny.database.SQLDatabase method) (pylogeny.database.SQLiteDatabase method) getTaxa() (pylogeny.alignment.alignment method) (pylogeny.alignment.phylipFriendlyAlignment method) getTree() (pylogeny.landscape.landscape method) (pylogeny.landscape.vertex method) getType() (pylogeny.rearrangement.rearrangement method) getVertex() (pylogeny.landscape.landscape method) graph (class in pylogeny.landscape)

H

hasPath() (pylogeny.landscape.graph method)

heuristic (class in pylogeny.heuristic)

I

indexOf() (pylogeny.landscape.landscape method) (pylogeny.tree.treeSet method) insert() (pylogeny.base.patriciaTree method) (pylogeny.base.trie method) insertRecord() (pylogeny.database.database method) insertRecords() (pylogeny.database.database method) invertAlongPathToNode() (in module pylogeny.newick) isBestImprovement() (pylogeny.landscape.vertex method) isEdge() (pylogeny.landscape.graph method) isEmpty() (pylogeny.database.database method) isExplored() (pylogeny.landscape.vertex method) isFailed() (pylogeny.landscape.vertex method) isInternalNode() (pylogeny.base.treeNode method) isLeaf() (pylogeny.base.treeNode method) isLocalOptimum() (pylogeny.landscape.landscape method) (pylogeny.landscape.vertex method) isNNI() (pylogeny.rearrangement.rearrangement method)

isSibling() (in module pylogeny.newick) isSPR() (pylogeny.rearrangement.rearrangement method) isTBR() (pylogeny.rearrangement.rearrangement method) isViolating() (pylogeny.landscape.landscape method) (pylogeny.landscape.vertex method) iterAllPathsOfBestImprovement() (pylogeny.landscape.landscape method) iterBipartitions() (pylogeny.landscape.vertex method) iterNNIForBranch() (pylogeny.rearrangement.topology method) iterNodes() (pylogeny.landscape.graph method) iterNonEmptyChildrenNodes() (pylogeny.base.trieNode method) iterRecords() (pylogeny.database.database method) iterSPRForBranch() (pylogeny.rearrangement.topology method) iterTrees() (pylogeny.tree.treeSet method) iterTypeForBranch() (pylogeny.rearrangement.topology method)

J

JSONWriter (class in pylogeny.JSONWriter)

L

landscape (class in pylogeny.landscape) landscapeParser (class in pylogeny.landscapeWriter) landscapeWriter (class in pylogeny.landscapeWriter) leaves() (pylogeny.base.treeStructure static method) likelihoodGreedy (class in pylogeny.heuristic)

lockBranch() (pylogeny.rearrangement.topology method) lockBranchFoundInTree() (pylogeny.landscape.landscape method) lockBranchFoundInTreeByIndex() (pylogeny.landscape.landscape method) longest_common_substring() (in module pylogeny.base)

M

median() (in module pylogeny.tree)

move() (pylogeny.rearrangement.topology method)

N

newickParser (class in pylogeny.newick) newTable() (pylogeny.database.database method) NNI() (pylogeny.rearrangement.topology method) node (class in pylogeny.newick) nodes() (pylogeny.base.treeStructure static method)

nodeToJSON() (pylogeny.JSONWriter.JSONWriter method) numberRootedTrees() (in module pylogeny.tree) numberUnrootedTrees() (in module pylogeny.tree) numEmptyChildrenNodes() (pylogeny.base.trieNode method)

P

parse() (pylogeny.landscapeWriter.landscapeParser method) (pylogeny.newick.newickParser method) (pylogeny.rearrangement.topology method) parseNewick() (in module pylogeny.newick) parsimonyGreedy (class in pylogeny.heuristic) ParsingError partitionModel (class in pylogeny.pll) path (pylogeny.heuristic.phylogeneticLinearHeuristic attribute) patriciaTree (class in pylogeny.base) phylipFriendlyAlignment (class in pylogeny.alignment) phylogeneticLinearHeuristic (class in pylogeny.heuristic) PhyloModelError postOrderTraversal() (pylogeny.base.treeStructure static method) profile_set (class in pylogeny.parsimony) pylogeny (module) pylogeny.alignment (module)

pylogeny.base (module) pylogeny.database (module) pylogeny.executable (module) pylogeny.heuristic (module) pylogeny.JSONWriter (module) pylogeny.landscape (module) pylogeny.landscapeWriter (module) pylogeny.model (module) pylogeny.newick (module) pylogeny.parsimony (module) pylogeny.pll (module) pylogeny.rearrangement (module) pylogeny.scoring (module) pylogeny.tree (module)

Q

query() (pylogeny.database.database method) (pylogeny.database.SQLDatabase method) (pylogeny.database.SQLiteDatabase method)

querymany() (pylogeny.database.database method) (pylogeny.database.SQLDatabase method) (pylogeny.database.SQLiteDatabase method)

R

raxml (class in pylogeny.executable) RAxMLIdentify (class in pylogeny.heuristic) rearrangement (class in pylogeny.rearrangement) RearrangementError recreateObject() (pylogeny.alignment.phylipFriendlyAlignment method) reinterpretNewick() (pylogeny.alignment.phylipFriendlyAlignment method) removeBranchLengths() (in module pylogeny.newick) removeTree() (pylogeny.landscape.landscape method) (pylogeny.tree.treeSet method) removeTreeByIndex() (pylogeny.landscape.landscape method)

removeUnaryInternalNodes() (in module pylogeny.newick) rerootToLeaf() (pylogeny.rearrangement.topology method) rspr (class in pylogeny.executable) RSPR_ALG_APPROX (pylogeny.executable.rspr attribute) RSPR_ALG_BB (pylogeny.executable.rspr attribute) RSPR_ALG_DEFAULT (pylogeny.executable.rspr attribute) RSPR_ALG_FPT (pylogeny.executable.rspr attribute) run() (pylogeny.executable.executable method) runFunction() (pylogeny.executable.raxml method)

S

scoreLikelihood() (pylogeny.landscape.vertex method) search() (pylogeny.base.patriciaTree method) (pylogeny.base.trie method) setAlignment() (pylogeny.landscape.landscape method) setChild() (pylogeny.base.treeBranch method) setChildNode() (pylogeny.base.trieNode method) setDefaultWeight() (pylogeny.landscape.graph method) setExplored() (pylogeny.landscape.vertex method) setLabel() (pylogeny.base.treeBranch method) setName() (pylogeny.tree.tree method) setOperator() (pylogeny.landscape.landscape method) setOrigin() (pylogeny.tree.tree method)

setParent() (pylogeny.base.treeBranch method) setScore() (pylogeny.tree.tree method) shuffleLeaves() (in module pylogeny.newick) site_profile (class in pylogeny.parsimony) smoothGreedy (class in pylogeny.heuristic) SPR() (pylogeny.rearrangement.topology method) SQLDatabase (class in pylogeny.database) SQLExhaustiveLandscape (class in pylogeny.database) SQLiteDatabase (class in pylogeny.database) SQLiteLandscape (class in pylogeny.database)

T

toDendroPy() (pylogeny.tree.tree method) toggleLock() (pylogeny.landscape.landscape method) toNewick() (pylogeny.rearrangement.rearrangement method) (pylogeny.rearrangement.topology method) (pylogeny.tree.tree method) topology (class in pylogeny.rearrangement) toProperNewickTreeSet() (pylogeny.landscape.landscape method) toStrList() (pylogeny.alignment.alignment method) toTopology() (pylogeny.rearrangement.rearrangement method) (pylogeny.tree.tree method) toTree() (pylogeny.rearrangement.rearrangement method) (pylogeny.rearrangement.topology method) toTreeFile() (pylogeny.tree.treeSet method) toTreeSet() (pylogeny.landscape.landscape method)

toUnrootedNewick() (pylogeny.rearrangement.topology method) toUnrootedTree() (pylogeny.rearrangement.topology method) tree (class in pylogeny.tree) treeBranch (class in pylogeny.base) treeNode (class in pylogeny.base) treepuzzle (class in pylogeny.executable) treeSet (class in pylogeny.tree) treeStructure (class in pylogeny.base) trie (class in pylogeny.base) trieNode (class in pylogeny.base)

U

updateNewick() (pylogeny.tree.tree method)

V

vertex (class in pylogeny.landscape)

W

weight() (pylogeny.parsimony.profile_set method) writeFile() (pylogeny.landscapeWriter.landscapeWriter method)

writeProperNexus() (pylogeny.alignment.phylipFriendlyAlignment method)