rerootTree - Reroot phylogenetic tree to have its germline sequence at a zero-length branch to a node which is the direct ancestor of the tree’s UCA. Assigns uca to be the ancestral node to the tree’s germline sequence, as germid as the tree’s germline sequence ID.

Description¶

Reroot phylogenetic tree to have its germline sequence at a zero-length branch to a node which is the direct ancestor of the tree’s UCA. Assigns uca to be the ancestral node to the tree’s germline sequence, as germid as the tree’s germline sequence ID.

Usage¶

rerootTree(tree, germline, min = 0.001, verbose = 1)

Arguments¶

tree

An ape phylo object

germline

ID of the tree’s predicted germline sequence

min

Maximum allowed branch length from germline to root

verbose

amount of rubbish to print

Value¶

phylo object rooted at the specified germline