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