anomalyZone: anomalyZone

In chutter/FilterZone: R Package For Detecting the Anomaly Zone and Alignment Filtering in Large Phylogenomic Datasets

Description

Applies the anomaly zone calculation across the entire tree (Degnan & Rosenberg 2006)

Usage

anomalyZone(tree = NULL, outgroups = NULL, print.node = TRUE)

Arguments

tree	phylogenetic tree read into R in phylo format
outgroups	outgroups to root your tree
print.node	prints the anomaly zone nodes if found

Value

a data.table of anomaly zone data calculated for all nodes in your tree

Examples

your.tree = ape::read.tree(file = "file-path-to-tree.tre")
astral.data = astralPlane(astral.tree = your.tree,
                          outgroups = c("species_one", "species_two"),
                          tip.length = 1)

chutter/FilterZone documentation built on Dec. 19, 2021, 4:07 p.m.