acctran: Assign edge length to tree

In KlausVigo/phangorn: Phylogenetic Reconstruction and Analysis

Assign edge length to tree

Description

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.

Author(s)

Klaus Schliep [e-mail]

See Also

pratchet

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)

KlausVigo/phangorn documentation built on Jan. 16, 2025, 1:08 p.m.