buildPhylo - Wrapper for alakazam::buildPhylipLineage

Description¶

Wrapper for alakazam::buildPhylipLineage

Usage¶

buildPhylo(
clone,
exec,
temp_path = NULL,
verbose = 0,
rm_temp = TRUE,
seq = "sequence",
tree = NULL,
onetree = TRUE
)

Arguments¶

clone

airrClone object

exec

dnapars or dnaml executable

temp_path

path to temporary directory

verbose

amount of rubbish to print

rm_temp

remove temporary files?

seq

sequece column in airrClone object

tree

fixed tree topology if desired (currently does nothing if specified)

onetree

Only sample one tree if multiple found.

Value¶

phylo object created by dnapars or dnaml with nodes attribute containing reconstructed sequences.