madRoot: Find The Root of a Phylogenetic Tree Using MAD Method

In orthGS: Orthology vs Paralogy Relationships among Glutamine Synthetase from Plants

Find The Root of a Phylogenetic Tree Using MAD Method

Description

Finds the root of an unrooted phylogenetic tree by minimizing the relative deviation from the molecular clock.

Usage

madRoot(tree, output_mode = 'phylo')

Arguments

tree	unrooted tree string in newick format or a tree object of class 'phylo'.
output_mode	amount of information to return. If 'phylo' (default) only the rooted tree is returned. If 'stats' also a structure with the ambiguity index, clock cv, the minimum ancestor deviation and the number of roots. If 'full' also an unrooted tree object, the index of the root branch, the branch ancestor deviations and a rooted tree object.

Details

This function is a slight modification of the code provided by Tria et al at https://www.mikrobio.uni-kiel.de/de/ag-dagan/ressourcen.

Value

a rooted tree and supplementary information if required.

Author(s)

Tria, F. D. K., Landan, G. and Dagan, T.

References

Tria, F. D. K., Landan, G. and Dagan, T. Nat. Ecol. Evol. 1, 0193 (2017).

Examples

## Not run: a <- msa(sequences=c("RAPGT", "KMPGT", "ESGGT"), ids = letters[1:3])$ali
rownames(a) <- letters[1:3]
tr <- mltree(a)$tree
rtr <- madRoot(tr)
## End(Not run)

orthGS documentation built on June 8, 2025, 12:37 p.m.