View source: R/tree.roguetaxa.R
tree.roguetaxa | R Documentation |
Implements the RogueNaRok algorithm for rogue taxon identification within phruta
tree.roguetaxa(folder = "3.Phylogeny", ...)
folder |
Name of the folder where the sequences to align are stored (character). |
... |
Arguments passed to |
None
## 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"
)
tree.roguetaxa(folder = "3.Phylogeny")
## End(Not run)
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