phangorn: parsimony – R documentation

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parsimony

Parsimony tree.

Description

parsimony returns the parsimony score of a tree using either the sankoff or the fitch algorithm. optim.parsimony tries to find the maximum parsimony tree using either Nearest Neighbor Interchange (NNI) rearrangements or sub tree pruning and regrafting (SPR). pratchet implements the parsimony ratchet (Nixon, 1999) and is the preferred way to search for the best tree. random.addition can be used to produce starting trees.

Usage

acctran(tree, data)

fitch(tree, data, site = "pscore")

random.addition(data, tree = NULL, method = "fitch")

parsimony(tree, data, method = "fitch", cost = NULL, site = "pscore")

sankoff(tree, data, cost = NULL, site = "pscore")

optim.parsimony(tree, data, method = "fitch", cost = NULL, trace = 1,
  rearrangements = "SPR", ...)

pratchet(data, start = NULL, method = "fitch", maxit = 1000,
  minit = 10, k = 10, trace = 1, all = FALSE, rearrangements = "SPR",
  perturbation = "ratchet", ...)

Arguments

`tree`	tree to start the nni search from.
`data`	A object of class phyDat containing sequences.
`site`	return either 'pscore' or 'site' wise parsimony scores.
`method`	one of 'fitch' or 'sankoff'.
`cost`	A cost matrix for the transitions between two states.
`trace`	defines how much information is printed during optimisation.
`rearrangements`	SPR or NNI rearrangements.
`...`	Further arguments passed to or from other methods (e.g. model="sankoff" and cost matrix).
`start`	a starting tree can be supplied.
`maxit`	maximum number of iterations in the ratchet.
`minit`	minimum number of iterations in the ratchet.
`k`	number of rounds ratchet is stopped, when there is no improvement.
`all`	return all equally good trees or just one of them.
`perturbation`	whether to use "ratchet", "random_addition" or "stochastic" (nni) for shuffling the tree.

Details

The "SPR" rearrangements are so far only available for the "fitch" method, "sankoff" only uses "NNI". The "fitch" algorithm only works correct for binary trees.

Value

parsimony returns the maximum parsimony score (pscore). optim.parsimony returns a tree after NNI rearrangements. pratchet returns a tree or list of trees containing the best tree(s) found during the search. acctran returns a tree with edge length according to the ACCTRAN criterion.

Author(s)

Klaus Schliep klaus.schliep@gmail.com

References

Felsenstein, J. (2004). Inferring Phylogenies. Sinauer Associates, Sunderland.

Nixon, K. (1999) The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis. Cladistics 15, 407-414

Examples

set.seed(3)
data(Laurasiatherian)
dm <- dist.hamming(Laurasiatherian)
tree <- NJ(dm)
parsimony(tree, Laurasiatherian)
treeRA <- random.addition(Laurasiatherian)
treeNNI <- optim.parsimony(tree, Laurasiatherian)
treeRatchet <- pratchet(Laurasiatherian, start=tree, maxit=100,
                        minit=5, k=5, trace=0)
# assign edge length
treeRatchet <- acctran(treeRatchet, Laurasiatherian)

plot(midpoint(treeRatchet))
add.scale.bar(0,0, length=100)

parsimony(c(tree,treeNNI, treeRatchet), Laurasiatherian)

phangorn

Phylogenetic Reconstruction and Analysis

v2.7.0

GPL (>= 2)

Authors

Klaus Schliep [aut, cre] (<https://orcid.org/0000-0003-2941-0161>), Emmanuel Paradis [aut] (<https://orcid.org/0000-0003-3092-2199>), Leonardo de Oliveira Martins [aut] (<https://orcid.org/0000-0001-5247-1320>), Alastair Potts [aut], Tim W. White [aut], Cyrill Stachniss [ctb], Michelle Kendall [ctb], Keren Halabi [ctb], Richel Bilderbeek [ctb], Kristin Winchell [ctb], Liam Revell [ctb], Mike Gilchrist [ctb], Jeremy Beaulieu [ctb], Brian O'Meara [ctb], Long Qu [ctb]

Initial release