Usage
parsimony(tree, data, method="fitch", ...)
optim.parsimony(tree, data, method="fitch", cost=NULL, trace=1,...)
pratchet(data, start=NULL, k=20, np=1, trace=1, all=FALSE, method="fitch", multicore=FALSE, ...)
fitch(tree, data, site = "pscore")
sankoff(tree, data, cost = NULL, site = "pscore")
CI(tree, data)
RI(tree, data)
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.
start
a starting tree can be supplied.
k
number of rounds in the ratchet.
np
number of (parallel) bootstraps (see details).
multicore
logical, if TRUE analysis is performed in parallel (see details).
all
return all equally good trees or just one of them.
...
Further arguments passed to or from other methods (e.g. model="sankoff" and cost matrix).