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,
...
)

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.