getBootstraps: Creates a bootstrap distribution for clone sequence alignments, and returns estimated trees for each bootstrap replicate as a nested list as a new input tibble column.

Description

getBootstraps Phylogenetic bootstrap function.

Usage

getBootstraps(
  clones,
  bootstraps,
  nproc = 1,
  bootstrap_nodes = TRUE,
  dir = NULL,
  id = NULL,
  build = "pratchet",
  exec = NULL,
  quiet = 0,
  rm_temp = TRUE,
  rep = NULL,
  seq = NULL,
  boot_part = "locus",
  by_codon = TRUE,
  starting_tree = FALSE,
  switches = FALSE,
  ...
)

Value

The input clones tibble with an additional column for the bootstrap replicate trees.

Arguments

clones: tibble airrClone objects, the output of formatClones
bootstraps: number of bootstrap replicates to perform
nproc: number of cores to parallelize computations
bootstrap_nodes: a logical if the the nodes for each tree in the trees column (required) should report their bootstrap value
dir: directory where temporary files will be placed (required if igphyml or dnapars specified)
id: unique identifer for this analysis (required if igphyml or dnapars specified)
build: program to use for tree building (phangorn, dnapars, igphyml)
exec: location of desired phylogenetic executable
quiet: amount of rubbish to print to console
rm_temp: remove temporary files (default=TRUE)
rep: current bootstrap replicate (experimental)
seq: column name containing sequence information
boot_part: is "locus" bootstrap columns for each locus separately
by_codon: a logical if the user wants to bootstrap by codon or by nucleotide. Default (codon based bootstrapping) is TRUE.
starting_tree: An indicator to use the existing trees column as the starting trees for RAxML
switches: a logical indicator to allow findSwitches to do permutations.
...: additional arguments to be passed to tree building program