Tree dating under treePL or — tree.dating • phruta

Performs tree dating under "treePL" or "PATHd-8" based on secondary calibrations. Note that "treePL" or "PATHd-8" must be installed in your PATH. How to install "PATHd-8" in mac "https://gist.github.com/cromanpa94/a43bc710a17220f71d796d6590ea7fe4" and "treePL" can be installed using homebrew (brew install brewsci/bio/treepl). Thanks to Brian O'Meara and Jonathan Chang, respectively.

Usage

tree.dating(
  taxonomyFolder = "1.CuratedSequences",
  phylogenyFolder = "3.Phylogeny",
  ...
)

Arguments

taxonomyFolder: Name of the folder where "1.Taxonomy.csv", created duing the "sq.curate" step, is stored (character).
phylogenyFolder: Name of the folder where "RAxML_bipartitions.phruta", created duing the "tree.raxml" step, is stored (character).
...: Arguments passed to "geiger::congruify.phylo".

Value

None

Examples

if (FALSE) {
sq.retrieve.direct(
  clades = c("Felis", "Vulpes", "Phoca"),
  species = "Manis_pentadactyla",
  genes = c("ADORA3", "CYTB")
)
sq.curate(
  filterTaxonomicCriteria = "Felis|Vulpes|Phoca|Manis",
  kingdom = "animals", folder = "0.Sequences"
)
sq.aln(folder = "1.CuratedSequences")
tree.raxml(
  folder = "2.Alignments", FilePatterns = "Masked",
  raxml_exec = "raxmlHPC", Bootstrap = 100,
  outgroup = "Manis_pentadactyla"
)
tree.dating(
  taxonomyFolder = "1.CuratedSequences",
  phylogenyFolder = "3.Phylogeny", scale = "treePL"
)
}