getBootstraps {dowser}

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,
  ...
)

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

Value

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