Index

_

__init__ (module)

A

AAThreeToOne() (in module sequtils) AddDots() (in module align) align (module) Align() (in module align)

AmbiguousNTCodes() (in module sequtils) ApplyToNodes() (in module tree) AssignMutations() (in module parse_tree) AssignTimes() (in module tree)

B

Base10Formatter() (in module plot) beast (module)

BuildSeqsFromMutsAndTips() (in module parse_tree)

C

CondenseSeqs() (in module sequtils)

CumulativeFractionPlot() (in module plot)

D

DatesPlot() (in module plot) DateToOrdinal() (in module sequtils)

DistanceAlongPath() (in module trajectory)

F

FindMotifs() (in module sequtils)

G

GetBalancedIndex() (in module tree) GetEntries() (in module sequtils) GetInfo() (in module tree) GetNewickTree() (tree.Tree method) GetNode() (in module tree)

GetPath() (in module tree) GetRoot() (tree.Tree method) GetSequence() (in module sequtils) GetTreeString() (in module parse_tree)

H

HeuristicTraceback() (in module trajectory)

I

IteratePaths() (in module trajectory)

L

ListsOfNodes() (in module tree)

M

MedianCredibleInterval() (in module stats)

N

Node (class in tree)

P

PairwiseStatistics() (in module align) parse_tree (module) ParseBoolValue() (in module src.io) ParseFileList() (in module src.io) ParseFloatValue() (in module src.io) ParseInfile() (in module src.io) ParseIntValue() (in module src.io)

ParseSeqValue() (in module src.io) ParseStringValue() (in module src.io) plot (module) PrintAllTreeInformation() (in module tree) PurgeAmbiguousDNA() (in module sequtils) PurgeDuplicates() (in module sequtils) PylabAvailable() (in module plot)

Q

QueryTree() (in module tree)

R

Read() (in module sequtils) ReadTreeTranslateBlock() (in module parse_tree) RecursivelyAssignDescendents() (in module tree) RecursivelyAssignSeqsFromMuts() (in module parse_tree) RecursivelyAssignTimes() (in module tree)

RecursivelySetNumbers() (in module tree) RecursivelySetTipAndInternalNumbers() (in module tree) RemoveDots() (in module align) ReverseComplement() (in module sequtils)

S

sequtils (module) SplitLabel() (in module plot) SplitNewick() (in module tree) src.io (module)

stats (module) StripGapsToFirstSequence() (in module align) StripLeadingTrailingGapsToFirstSequence() (in module align)

T

TallySiteChangesAlongTree() (in module tree) TraceMutationPath() (in module parse_tree) Trajectory (class in trajectory) trajectory (module)

Translate() (in module sequtils) Tree (class in tree) tree (module)

U

UnknownsToGaps() (in module sequtils)

W

Write() (in module sequtils) WriteGraphVizTrajectory() (in module trajectory) WriteMutationDates() (in module trajectory) WriteNewick() (tree.Tree method)

WriteNEXUS() (in module sequtils) WriteNodePersistence() (in module trajectory) WriteXML() (in module beast)