tqdist_QuartetDistance {Quartet}R Documentation

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

Author(s)

Martin R. Smith, after Andreas Sand

References

Sand A, Holt MK, Johansen J, Brodal GS, Mailund T, Pedersen CNS (2014). “tqDist: a library for computing the quartet and triplet distances between binary or general trees.” Bioinformatics, 30(14), 2079–2080. ISSN 1460-2059, doi:10.1093/bioinformatics/btu157.


[Package Quartet version 1.2.6 Index]