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.
getBootstraps Phylogenetic bootstrap function.
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, ... )
airrCloneobjects, the output of formatClones
- number of bootstrap replicates to perform
- number of cores to parallelize computations
- a logical if the the nodes for each tree in the trees column (required) should report their bootstrap value
- directory where temporary files will be placed (required
- unique identifer for this analysis (required if
- program to use for tree building (phangorn, dnapars, igphyml)
- location of desired phylogenetic executable
- amount of rubbish to print to console
- remove temporary files (default=TRUE)
- current bootstrap replicate (experimental)
- column name containing sequence information
- is “locus” bootstrap columns for each locus separately
- a logical if the user wants to bootstrap by codon or by nucleotide. Default (codon based bootstrapping) is TRUE.
- An indicator to use the existing trees column as the starting trees for RAxML
- a logical indicator to allow findSwitches to do permutations.
- additional arguments to be passed to tree building program
The input clones tibble with an additional column for the bootstrap replicate trees.