ReducedStrictConsensus

by Tobias Hill, implementing methods by Mark Wilkinson

class Reduced(inThing=None, skip=0, max=None)

listOfSplits(treatMultifurcatingRootsAsUnrooted, minimumProportion=1.0)

listOfSplits will return a list of splits (maybe zero lenght) that fulfill the minimumProportion criterion

majorityRuleConsensus()

reducedConsensusProfile()

reducedConsensusProfile will depending on the minimumProportion and the input data produce 4 different outputs. * Given a set of trees with identical leafsets and a minimumProportion=1.0 a reduced strict consensus tree will be produced, i.e. a tree where all splits can be found in all input trees * Given a set of trees with identical leafsets and a 1.0 < minimumProportion >= 0.5 a reduced majority profile will be produced, i.e. a set of trees defined on differing leafsets with differing support, this profile will include the reduced strict consensus tree if it exists * Given a set of trees with differing leafsets and a minimumProportion= 1.0 a reduced strict super tree will be produced, i.e. a tree where all splits can be found in all input trees * Given a set of trees with differing leafsets and a 1.0 < minimimProportion >= 0.5 a reduced majority supertree profile will be produced, i.e. a set of trees defined on differing leafsets with differing support, this profile will include the reduced strict supertree tree if it exists

reducedMemQuick()

reducedQuick()

reducedStrictConsensus()

writeExtended(extendedFileName='rcExtended')

writeIntersections(filename='rcIntersections')