Skip to contents

Direct entry points to "tqDist" functions

Source: R/cpdt.R, R/tqDist.r
Distances.Rd

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

Usage

# S3 method for class 'phylo'
TripletDistance(tree1, tree2 = NULL)

# S3 method for class 'list'
TripletDistance(tree1, tree2 = NULL)

# S3 method for class 'multiPhylo'
TripletDistance(tree1, tree2 = NULL)

QuartetDistance(file1, file2)

QuartetAgreement(file1, file2)

PairsQuartetDistance(file1, file2)

OneToManyQuartetAgreement(file1, file2)

AllPairsQuartetDistance(file)

AllPairsQuartetAgreement(file)

TripletDistance(tree1, tree2 = NULL)

# S3 method for class 'character'
TripletDistance(tree1, tree2 = NULL)

PairsTripletDistance(file1, file2)

AllPairsTripletDistance(file)

Arguments

tree1, tree2

Arguments to TripletDistance: file paths containing Newick trees, phylogenetic trees of class phylo, or lists/multiPhylo of trees. If tree1 is a list and tree2 = NULL, returns a distance matrix of all pairwise distances.

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:

  • A, resolved in the same fashion in both trees;

  • E, unresolved in both trees.

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

  • TripletDistance(phylo): Triplet distance between two trees of class phylo. Uses the CPDT algorithm (Jansson and Rajaby 2017) .

  • TripletDistance(list): Triplet distance between each pair of trees in a list. If tree2 is provided, returns pairwise distances between corresponding trees in tree1 and tree2. If tree2 = NULL, returns a distance matrix of all pairwise distances within tree1.

  • TripletDistance(multiPhylo): Triplet distance between each pair of trees in a multiPhylo object.

  • QuartetDistance(): Returns the quartet distance between the tree. in file1 and the tree in file2.

  • QuartetAgreement(): Returns a vector of length two, listing [1] the number of resolved quartets that agree (A); [2] the number of quartets that are unresolved in both trees (E). See Brodal et al. (2013) .

  • PairsQuartetDistance(): Quartet distance between the tree on each line of file1 and the tree on the corresponding line of file2.

  • OneToManyQuartetAgreement(): Quartet distance between the tree in file1 and the tree on each line of file2.

  • AllPairsQuartetDistance(): Quartet distance between each tree listed in file and each other tree therein.

  • AllPairsQuartetAgreement(): Quartet status for each pair of trees in file.

  • TripletDistance(): Triplet distance between trees. tree1 and tree2 can be phylo objects, file paths to Newick tree files, or lists/multiPhylo objects. If tree1 is a list and tree2 = NULL, computes all pairwise distances; if both are lists, computes distances between corresponding pairs. Uses the CPDT algorithm (Jansson and Rajaby 2017) .

  • TripletDistance(character): Triplet distance between single trees read from Newick-format files tree1 and tree2.

  • PairsTripletDistance(): Triplet distance between the tree on each line of file1 and the tree on the corresponding line of file2.

  • AllPairsTripletDistance(): Triplet distance between each tree listed in file and each other tree therein.

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.

Jansson J, Rajaby R (2017). “A More Practical Algorithm for the Rooted Triplet Distance.” Journal of Computational Biology, 24(2), 106–126. doi:10.1089/cmb.2016.0185 .

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 .

See also

  • QuartetStatus() takes trees, rather than files, as input.

  • TQFile() creates a temporary file containing specified trees.

Other TQDist functions: TQDist()

Author

  • Quartet algorithms: Brodal et al. (2013) ; Holt et al. (2014) . C implementation: Sand et al. (2014) ; modified for portability by Martin R. Smith.

  • Triplet algorithm: Jansson and Rajaby (2017) . C++ implementation by Ramesh Rajaby; R integration by Martin R. Smith.