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. CI and RI computes the consistency and retention index.

Usage

parsimony(tree, data, method="fitch", ...)
optim.parsimony(tree, data, method="fitch", cost=NULL, trace=1, rearrangements="SPR", ...)
pratchet(data, start=NULL, method="fitch", maxit=1000, k=10, trace=1, all=FALSE,  rearrangements="SPR", perturbation="ratchet", ...)
fitch(tree, data, site = "pscore")
sankoff(tree, data, cost = NULL, site = "pscore")
random.addition(data, method="fitch")
CI(tree, data, cost = NULL, sitewise=FALSE)
RI(tree, data, cost = NULL, sitewise=FALSE)
acctran(tree, data)

Arguments

data

A object of class phyDat containing sequences.

tree

tree to start the nni search from.

method

one of 'fitch' or 'sankoff'.

cost

A cost matrix for the transitions between two states.

site

return either 'pscore' or 'site' wise parsimony scores.

trace

defines how much information is printed during optimisation.

rearrangements

SPR or NNI rearrangements.

start

a starting tree can be supplied.

maxit

maximum number of iterations in the ratchet.

number of rounds ratchet is stopped, when there is no improvement.

all

return all equally good trees or just one of them.

perturbation

whether using a ratchet or stochastic (nni) for shuffling the tree.

...

Further arguments passed to or from other methods (e.g. model="sankoff" and cost matrix).

sitewise

return CI/RI for alignment or sitewise

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.

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.

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

Run this code

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, k=5)
# assign edge length
treeRatchet <- acctran(treeRatchet, Laurasiatherian)

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

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

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