Infer microsynteny-based phylogeny with IQTREE

Usage

infer_microsynteny_phylogeny(
  transposed_profiles = NULL,
  bootr = 1000,
  alrtboot = 1000,
  threads = "AUTO",
  model = "MK+FO+R",
  outdir = tempdir(),
  outgroup = NULL,
  verbose = FALSE
)

Arguments

transposed_profiles: A binary and transposed profile matrix. The profile matrix can be obtained with phylogenomic_profile().
bootr: Numeric scalar with the number of bootstrap replicates. Default: 1000.
alrtboot: Numeric scalar with the number of replicates for the SH-like approximate likelihood ratio test. Default: 1000.
threads: Numeric scalar indicating the number of threads to use or "AUTO", which allows IQTREE to automatically choose the best number of threads to use. Default: "AUTO".
model: Substitution model to use. If you are unsure, pick the default. Default: "MK+FO+R".
outdir: Path to output directory. By default, files are saved in a temporary directory, so they will be deleted when the R session closes. If you want to keep the files, specify a custom output directory.
outgroup: Name of outgroup clade to group the phylogeny. Default: NULL (unrooted phylogeny).
verbose: Logical indicating if progress messages should be prompted. Default: FALSE.

Value

A character vector of paths to output files.

Examples

data(clusters)
profile_matrix <- phylogenomic_profile(clusters)
tmat <- binarize_and_transpose(profile_matrix)

# Leave only some legumes and P. mume as an outgroup for testing purposes
included <- c("gma", "pvu", "vra", "van", "cca", "pmu")
tmat <- tmat[rownames(tmat) %in% included, ]

# Remove non-variable sites
tmat <- tmat[, colSums(tmat) != length(included)]

if(iqtree_is_installed()) {
    phylo <- infer_microsynteny_phylogeny(tmat, outgroup = "pmu", 
                                          threads = 1)
}