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Quartet (version 1.2.6)

tqdist_QuartetDistance: Direct entry points to 'tqDist' functions

Description

Functions to calculate triplet and quartet distances between pairs of trees. Input is not checked for sanity.

Usage

tqdist_QuartetDistance(file1, file2)
tqdist_QuartetAgreement(file1, file2)
tqdist_QuartetAgreementEdge(edge1, edge2)
tqdist_QuartetAgreementChar(string1, string2)
tqdist_PairsQuartetDistance(file1, file2)
tqdist_OneToManyQuartetAgreement(file1, fileMany)
tqdist_OneToManyQuartetAgreementChar(tree, trees)
tqdist_OneToManyQuartetAgreementEdge(edge, edges)
tqdist_AllPairsQuartetDistance(file)
tqdist_AllPairsQuartetDistanceChar(string)
tqdist_AllPairsQuartetDistanceEdge(edges)
tqdist_AllPairsQuartetAgreement(file)
tqdist_AllPairsQuartetAgreementChar(string)
tqdist_AllPairsQuartetAgreementEdge(edges)
tqdist_TripletDistance(file1, file2)
tqdist_PairsTripletDistance(file1, file2)
tqdist_AllPairsTripletDistance(file)

Value

The distance between the requested trees.

Arguments

file, file1, file2

Paths to files containing a tree or trees in Newick format.

Functions

  • tqdist_QuartetAgreement(): Agreement of each quartet

  • tqdist_QuartetAgreementEdge(): Agreement of each quartet

  • tqdist_QuartetAgreementChar(): Agreement of each quartet

  • tqdist_PairsQuartetDistance(): Distance between pairs

  • tqdist_OneToManyQuartetAgreement(): Distance between pairs

  • tqdist_OneToManyQuartetAgreementChar(): Distance between pairs

  • tqdist_OneToManyQuartetAgreementEdge(): Distance between pairs

  • tqdist_AllPairsQuartetDistance(): Distance between all pairs

  • tqdist_AllPairsQuartetDistanceChar(): Distance between all pairs

  • tqdist_AllPairsQuartetDistanceEdge(): Distance between all pairs

  • tqdist_AllPairsQuartetAgreement(): Agreement between all pairs of trees

  • tqdist_AllPairsQuartetAgreementChar(): Agreement between all pairs of trees

  • tqdist_AllPairsQuartetAgreementEdge(): Agreement between all pairs of trees

  • tqdist_TripletDistance(): Triplet distance between two trees

  • tqdist_PairsTripletDistance(): Triplet distance between pairs

  • tqdist_AllPairsTripletDistance(): Triplet distance between all pairs

Author

Martin R. Smith, after Andreas Sand

Details

Functions are called from R with user-friendly functions such as AllPairsQuartetDistance.

References

Sand2014Quartet