Distances {Quartet}R Documentation

Direct entry points to "tqDist" functions

Description

Wrappers for functions in "tqDist", which calculate triplet and quartet distances between pairs of trees.

Usage

QuartetDistance(file1, file2)

QuartetAgreement(file1, file2)

PairsQuartetDistance(file1, file2)

OneToManyQuartetAgreement(file1, file2)

AllPairsQuartetDistance(file)

AllPairsQuartetAgreement(file)

TripletDistance(file1, file2)

PairsTripletDistance(file1, file2)

AllPairsTripletDistance(file)

Arguments

file, file1, file2

Paths to files containing a tree or trees in Newick format, possibly created using TQFile().

Value

...Distance() functions return the distance between the requested trees.

...Agreement() functions return the number of triplets or quartets that are:

Comparing a tree against itself yields the totals (A+B+C) and (D+E) referred to by Brodal et al. (2013) and Holt et al. (2014).

Functions

Author(s)

References

Brodal GS, Fagerberg R, Mailund T, Pedersen CNS, Sand A (2013). “Efficient algorithms for computing the triplet and quartet distance between trees of arbitrary degree.” SODA '13 Proceedings of the Twenty-Fourth Annual ACM-SIAM Symposium on Discrete Algorithms, 1814–1832. doi:10.1137/1.9781611973105.130.

Holt MK, Johansen J, Brodal GS (2014). “On the scalability of computing triplet and quartet distances.” In Proceedings of 16th Workshop on Algorithm Engineering and Experiments (ALENEX) Portland, Oregon, USA.

See Also


[Package Quartet version 1.2.7 Index]