Resolve polytomies to have the minimum number of single timepoint clades
resolvePolytomies(
phy,
clone,
minlength = 0.001,
time = "time",
sequence = "sequence_id",
germline = "Germline",
verbose = FALSE
)A phylo tree object in which polytomies are resolved to
have the minimum number of single timepoint clades.
Tree object
airrClone data object corresponding to phy
Branch lengths to collapse in trees
Column name holding numeric time information
Column name holding sequence ID
Germline sequence name
Print lots of rubbish while running?
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.
Uses output from getTrees during correlationTest.