Assign edge length to tree

parsimony_edgelength and acctran assign edge length to a tree where the edge length is the number of mutations. parsimony_edgelengths assigns edge lengths using a joint reconstruction based on the sankoff algorithm. Ties are broken at random and trees can be multifurating. acctran is based on the fitch algorithm and is faster. However trees need to be bifurcating and ties are split.

Usage

acctran(tree, data)

parsimony_edgelength(tree, data)

Arguments

tree

a tree, i.e. an object of class pml

data

an object of class phyDat

Value

a tree with edge length.

See also

pratchet

Author

Klaus Schliep klaus.schliep@gmail.com

Examples

data(Laurasiatherian)
# lower number of iterations for the example, to run time less than 5 sec.
treeRatchet <- pratchet(Laurasiatherian, minit=5, k=5, trace=0)
# assign edge length (number of substitutions)
treeRatchet <- parsimony_edgelength(treeRatchet, Laurasiatherian)
plot(midpoint(treeRatchet))
add.scale.bar(0,0, length=100)