resolvePolytomies: Resolve polytomies to have the minimum number of single...

In dowser: B Cell Receptor Phylogenetics Toolkit

Resolve polytomies to have the minimum number of single timepoint clades

Description

Resolve polytomies to have the minimum number of single timepoint clades

Usage

resolvePolytomies(
  phy,
  clone,
  minlength = 0.001,
  time = "time",
  sequence = "sequence_id",
  germline = "Germline",
  verbose = FALSE
)

Arguments

phy	Tree object
clone	airrClone data object corresponding to phy
minlength	Branch lengths to collapse in trees
time	Column name holding numeric time information
sequence	Column name holding sequence ID
germline	Germline sequence name
verbose	Print lots of rubbish while running?

Details

Iteratively identifies polytomies (clusters of < minlength branches), prunes each descendant branch, combines clades with the same timepoint before grouping them back together. Checks to make sure that the divergence of each tip is the same after resolution.

Value

A phylo tree object in which polytomies are resolved to have the minimum number of single timepoint clades.

See Also

Uses output from getTrees during correlationTest.

dowser documentation built on May 29, 2024, 3:06 a.m.