treeCompare function

Visualize the difference between phylogenetic trees

The function scans a pair of phylogenetic trees to find topological differences.

treeCompare(tree,tree1,focal=NULL,plot=TRUE)

Arguments

• tree, tree1: a phylogenetic tree. The tree needs not to be ultrametric and fully dichotomous. Generic name and specific epithet must be separated by '_'.
• focal: a vector of focal species to search on both tree and tree1.
• plot: if TRUE, the function produces an interactive plotting device to check differences in species placement at the genus level.

Returns

The function returns a data-frame indicating for each un-matching/focal species its sister species/clades on both trees.

Examples

## Not run:

DataFelids$tree->treefel

set.seed(22)
drop.tip(treefel,sample(treefel$tip.label,20))->tree.red
swapONE(tree.red,si=0.5)[[1]]->tree.red

sample(tree.red$tip.label,10)->focal.species

treeCompare(treefel,tree.red)->comp
treeCompare(treefel,tree.red,focal=focal.species)->comp1
## End(Not run)

Author(s)

Giorgia Girardi, Silvia Castiglione, Carmela Serio, Antonella Esposito