Wrapper to run last from an R session

Usage

run_last(
  seq = NULL,
  verbose = FALSE,
  outdir = tempdir(),
  threads = 1,
  compare = "all",
  lastD = 1e+06,
  ...
)

seq: A processed list of AAStringSet objects as returned by process_input().
verbose: Logical indicating if progress messages should be printed. Default: FALSE.
outdir: Output directory for last results. By default, output files are saved to a temporary directory.
threads: Number of threads to use. Default: 1.
compare: Character scalar indicating which comparisons should be made when running last. Possible modes are "all" (all-vs-all comparisons), "intraspecies" (intraspecies comparisons only), or "interspecies" (interspecies comparisons only). Alternatively, users can pass a 2-column data frame as input with the names of species to be compared.
lastD: last option D: query letters per random alignment. Default: 1e6.
...: Any additional arguments to lastal.

A list of data frames containing last's tabular output for each pairwise combination of species. For n species, the list length will be \(n^2\).

data(proteomes)
data(annotation)
seq <- process_input(proteomes, annotation)$seq[1:2]
if(last_is_installed()) {
    last_results <- run_last(seq)
}