Description Usage Arguments Value Author(s) References Examples
This function estimates the proportion of edges to be assigned to regimes based on ancestral regime reconstruction (Yang et al. 1995; Pupko et al. 2000; Paradis et al. 2004; Revell 2012).
1 | paint.edges(tree, species.groups, average.nodes = TRUE, root.edge = TRUE)
|
tree |
An object of class |
species.groups |
A named factor assigning species to regimes. |
average.nodes |
Whether or not to average reconstructed probabilities of regime states from parent and daughter nodes for tree edges. |
root.edge |
Whether or not to return a root edge. |
A matrix of dimension nedge-by-nregimes. NOTE: edges are in postorder.
Eric W. Goolsby
Paradis E., Claude J., Strimmer K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics. 20:289.290.
Pupko T., Pe'er I., Shamir R., Graur D. 2000. A fast algorithm for joint reconstruction of ancestral amino acid sequences. Molecular Biology and Evolution. 17:890-896.
Yang Z., Kumar S., Nei, M. 1995. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics. 141:1641-1650.
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