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
-
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
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.