tqdist_QuartetDistance: Direct entry points to 'tqDist' functions

In ms609/SlowQuartet: Comparison of Phylogenetic Trees Using Quartet and Split Measures

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)

Arguments

file, file1, file2

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

Details

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

Value

The distance between the requested trees.

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(s)

Martin R. Smith, after Andreas Sand

References

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Sand2014Quartet

ms609/SlowQuartet documentation built on April 22, 2024, 5:41 p.m.