P4 Classes and Modules

P4 is a phyloinformatic toolkit that implements tree-heterogeneous models. Here we have the main classes and modules that might be useful to the user.

The code is hosted at GitHub.

Return to the main p4 docs page

• Index

• Python Module Index

• Alignment
  • Alignment
• Constraints
  • Constraints
• Data
  • Data
• DistanceMatrix
  • DistanceMatrix
• GeneticCode
  • GeneticCode
• Model
  • Model
• Mcmc
  • Mcmc
• McmcCheckPointReader
  • McmcCheckPointReader
• NexusSets
  • NexusSets
• Node
  • Node
• Numbers
  • Numbers
• PosteriorSamples
  • PosteriorSamples
• QuartetJoining
  • QuartetJoining
• ReducedStrictConsensus
  • Reduced
• Sequence
  • Sequence
• SequenceList
  • SequenceList
• SuperTreeSupport
  • SuperTreeSupport
• Tree
  • RMatrix
  • Gdasrv
  • Comp
  • PInvar
  • Tree
• TreeFileLite
  • TreeFileLite
• TreePartitions
  • TreePartitions
• Trees
  • Trees
• func
  • _compareSplitsBetweenTwoTreePartitions()
  • _stdErrorOfTheDifferenceBetweenTwoMeans()
  • _sumOfColumns()
  • _sumOfRows()
  • _sumOfSquares()
  • charsets()
  • chiSquaredProb()
  • compareSplitsBetweenTreePartitions()
  • dirichlet1()
  • dirichlet2()
  • dump()
  • effectiveSampleSize()
  • factorial()
  • fixCharsForLatex()
  • getProteinEmpiricalModelComp()
  • getProteinEmpiricalModelRMatrix()
  • getSplitKeyFromTaxNames()
  • getSplitStringFromKey()
  • gsl_meanVariance()
  • gsl_ran_dirichlet()
  • gsl_ran_gamma()
  • isDnaRnaOrProtein()
  • ls()
  • maskFromNexusCharacterList()
  • matrixLowerTriangleToUpperTriangle()
  • mean()
  • nChooseK()
  • nRootedTrees()
  • nRootedTreesWithMultifurcations()
  • nUnrootedTrees()
  • nUnrootedTreesWithMultifurcations()
  • newEmptyAlignment()
  • newtonRaftery94_eqn16()
  • nexusCheckName()
  • nexusFixNameIfQuotesAreNeeded()
  • nexusUnquoteAndDeUnderscoreName()
  • nexusUnquoteName()
  • polar2square()
  • randomTree()
  • read()
  • readAndPop()
  • readFile()
  • readJplace()
  • recipes()
  • reseedCRandomizer()
  • setTerminalColor()
  • setTerminalColour()
  • sortListOfListsOnListElementNumber()
  • sortListOfObjectsOn2Attributes()
  • sortListOfObjectsOnAttribute()
  • spaceDelimitedToTabDelimited()
  • splash()
  • splash2()
  • square2polar()
  • stringZapWhitespaceAndDigits()
  • studentsTStat()
  • studentsTTest1()
  • summarizeMcmcPrams()
  • tailAreaProbability()
  • unPickleMcmc()
  • unPickleSTMcmc()
  • uninstall()
  • uniqueFile()
  • unsetTerminalColor()
  • unsetTerminalColour()
  • variance()
  • versionAsDate()
  • versionAsGitHash()
  • which()
  • which2()
  • writeInColor()
  • writeInColour()
  • xSquared()
• Var
  • Var
• mrp
  • mrp()
  • reverseMrp()