iqtree: Run IQ-TREE
In joelnitta/jntools: Joel Nitta's R Tools

Description Usage Arguments Value Examples

For details, see http://www.iqtree.org/doc/

iqtree(
  alignment = NULL,
  wd = getwd(),
  aln_path = NULL,
  tree_path = NULL,
  bb = NULL,
  nt = NULL,
  alrt = NULL,
  m = NULL,
  redo = FALSE,
  spp = NULL,
  seed = NULL,
  echo = FALSE,
  other_args = NULL,
  ...
)

`alignment`	DNA alignment to use for phylogenetic analysis. Must be matrix (i.e., aligned sequences) of class DNAbin
`wd`	Path to working directory. The alignment and IQ-TREE intermediate files and results will be written here.
`aln_path`	Path to DNA alignment. Either alignment, or aln_path must be provided, but not both
`tree_path`	Optional; path to tree when it is written out by IQ-TREE, useful if this differs from default alignment name.
`bb`	Optional; number of ultrafast bootstrap replicates to run.
`nt`	Optional; number of cores to use. Set to "AUTO" to determine automatically.
`alrt`	Optional; number of SH-aLRT tests to run.
`m`	Optional; specify model. If no model is given, ModelTest will be run to identify the best model for the data.
`redo`	Logical; should the analysis be redone from scratch if output from previous runs is present?
`spp`	Path to partition file.
`seed`	Optional; Specify a random number seed to reproduce a previous run.
`echo`	Logical; should STDERR be written to the screen?
`other_args`	Other arguments to pass to IQ tree; must be entered as a character vector with the name and value of each argument separately. For example, c("-pers", "0.2", "-nstop", "500").
`...`	Additional arguments; not used by this function.

Phylogenetic tree (list of class "phylo")

## Not run: 
library(ape)
data(woodmouse)
# Rapid boot-strap tree with 1000 replicates on best-fitting model
tree <- iqtree(woodmouse, tempdir(), bb = 1000, echo = TRUE)
plot(tree)
# Check the optimum number of cores to use for GTR+I+G model
iqtree(tempdir(), woodmouse, m = "GTR+I+G", nt = "AUTO", echo = TRUE, redo = TRUE)

## End(Not run)