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Run Partitionfinder v.1

Source: R/sq.partitionfinderv1.R
sq.partitionfinderv1.Rd

This function runs partitionfinder v1 within phruta. For now, all analyses are based on genes. Please note that you need at least two gene regions to run partitionfinder.

Usage

sq.partitionfinderv1(
  folderAlignments = "2.Alignments",
  FilePatterns = "Masked",
  folderPartitionFinder = "2.1.PartitionFinderv1",
  models = "all",
  run = TRUE
)

Arguments

folderAlignments

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 analyzed.

folderPartitionFinder

Name of the new folder where the output files are stored (string).

models

Models to run in partitionfinder (string).

run

Run partitionfinder?

Value

None

Examples

if (FALSE) { # \dontrun{
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")
sq.partitionfinderv1(
  folderAlignments = "2.Alignments",
  FilePatterns = "Masked",
  models = "all"
)
} # }