tree.raxml: Tree inference under RAxML

In cromanpa94/phruta: Phylogenetic Reconstruction and Time-dating

Tree inference under RAxML

Description

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

## Not run: 
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"
)

## End(Not run)

cromanpa94/phruta documentation built on July 7, 2024, 4:58 p.m.