Tree inference under RAxML — tree.raxml • phruta

Performs tree inference under "RAxML" for aligned fasta sequences in a given folder (default is "2.Alignments"). Note that you need at least two gene regions to run a partitioned analysis.

Usage

tree.raxml(
  folder = "2.Alignments",
  FilePatterns = "Masked_",
  raxml_exec = "raxmlHPC",
  Bootstrap = 100,
  outgroup,
  partitioned = FALSE,
  ...
)

Arguments

folder: Name of the folder where the sequences to align are stored (character).
FilePatterns: A string that is common to all the target files in the relevant folder (character). Note that this argument can be set to "NULL" if no specific pattern wants to be analized.
raxml_exec: Where to find "RAxML" or how to run it from the console? (string).
Bootstrap: Number of bootstrap replicates (numeric).
outgroup: A single string of comma-separated tip labels to be used as outgroup in "RAxML" See "RAxML" documentation for more details (character).
partitioned: Whether analyses should be partitioned by gene (Logical).
...: Arguments passed to "ips::raxml".

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"
)
}