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Tree inference under RAxML

Source: R/tree.constraint.R
tree.constraint.Rd

Performs tree inference under "RAxML" for aligned fasta sequences in a given folder (default is "2.Alignments").

Usage

tree.constraint(
  taxonomy_folder = "1.CuratedSequences",
  targetColumns = c("kingdom", "phylum", "class", "order", "family", "genus",
    "species_names"),
  Topology = "((ingroup), outgroup);",
  outgroup = NULL
)

Arguments

taxonomy_folder

Name of the folder where the 1.Taxonomy file is stored.

targetColumns

Where to find "RAxML" or how to run it from the console? (string).

Topology

A string summarizing the desired topological constraint in newick format.

outgroup

Optional and only required when the topology argument is not "((ingroup), outgroup);".

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"
)

tree.constraint(
  taxonomy_folder = "1.CuratedSequences",
  targetColumns = c("kingdom", "phylum", "class", "order", "family",
  "genus", "species_names"),
  Topology = "((ingroup), outgroup);",
  outgroup = "Manis_pentadactyla"
)
tree.constraint(
  taxonomy_folder = "1.CuratedSequences",
  targetColumns = c("kingdom", "phylum", "class", "order", "family",
  "genus", "species_names"),
  Topology = "((Felis), (Phoca));"
)
}