View source: R/sq.partitionfinderv1.R
sq.partitionfinderv1 | R Documentation |
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.
sq.partitionfinderv1(
folderAlignments = "2.Alignments",
FilePatterns = "Masked",
folderPartitionFinder = "2.1.PartitionFinderv1",
models = "all",
run = TRUE
)
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 |
folderPartitionFinder |
Name of the new folder where the output files are stored (string). |
models |
Models to run in partitionfinder (string). |
run |
Run partitionfinder? |
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")
sq.partitionfinderv1(
folderAlignments = "2.Alignments",
FilePatterns = "Masked",
models = "all"
)
## End(Not run)
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