Description Details Author(s) References Examples

Computation of Colless-Like, Sackin and cophenetic balance indices of a phylogenetic tree and study of the distribution of these balance indices under the alpha-gamma model. For more details see A. Mir, F. Rossello, L. Rotger (2013) <doi:10.1016/j.mbs.2012.10.005>, M. J. Sackin (1972) <doi:10.1093/sysbio/21.2.225>, D. H. Colless (1982) <doi:10.2307/2413420>.

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Arnau Mir, Francesc Rossello, Lucia Rotger

Maintainer: Lucia Rotger <[email protected]>

B. Chen, D. Ford, M. Winkel, A new family of Markov branching trees: the alpha-gamma model. *Electr. J. Probab*. **14** (2009), 400-430.

A. Mir, F. Rossello, L. Rotger, A Colless-like balance index for multifurcating phylogenetic trees.

A. Mir, F. Rossello, L. Rotger, A new balance index for phylogenetic trees. *Mathematical Biosciences* **241** (2013), 125-136.

M. J. Sackin, "Good" and "bad" phenograms. *Sys. Zool*, **21** (1972), 225-226.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ```
# A random phylogenetic tree of 5 leaves between all trees with 5 leaves
# following the alpha-gamma model with alpha=0.5 and gamma=0.3
a.g.tree = a.g.model(5,0.5,0.3)
# To compute the percentile of that tree of the Colless-Like,
# Sackin and cophenetic normalized balance indices under the alpha-gamma
# model with alpha=0.5 and gamma=0.3, and a distribution plot.
#distribution(a.g.tree,0.5,0.3,db.path=getwd())
# For a percentile plot set the parameter percentile.plot as TRUE
#distribution(a.g.tree,0.5,0.3,db.path=getwd(),percentile.plot=TRUE)
# Computation of the Colless-Like, Sackin and cophenetic balance indices
# of a sample of 50 trees that follow the alpha-gamma distribution
# with alpha=0.5 and gamma=0.3 with 5 leaves.
indices.data = indices.simulation(5,0.5,0.3,50)
# Computation of the percentile of the random tree using the previous
# generated sample
distribution(a.g.tree,0.5,0.3,set.indices=indices.data)
``` |

LuciaRotger/CollessLike documentation built on April 18, 2018, 11:07 p.m.

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