View source: R/tree.constraint.R
tree.constraint | R Documentation |
Performs tree inference under "RAxML"
for aligned fasta sequences in
a given folder (default is "2.Alignments"
).
tree.constraint(
taxonomy_folder = "1.CuratedSequences",
targetColumns = c("kingdom", "phylum", "class", "order", "family", "genus",
"species_names"),
Topology = "((ingroup), outgroup);",
outgroup = NULL
)
taxonomy_folder |
Name of the folder where the 1.Taxonomy file is stored. |
targetColumns |
Where to find |
Topology |
A string summarizing the desired topological constraint in newick format. |
outgroup |
Optional and only required when the topology argument is not "((ingroup), outgroup);". |
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"
)
tree.constraint(
taxonomy_folder = "1.CuratedSequences",
targetColumns = c("kingdom", "phylum", "class", "order", "family",
"genus", "species_names"),
Topology = "((ingroup), outgroup);",
outgroup = "Manis_pentadactyla"
)
tree.constraint(
taxonomy_folder = "1.CuratedSequences",
targetColumns = c("kingdom", "phylum", "class", "order", "family",
"genus", "species_names"),
Topology = "((Felis), (Phoca));"
)
## End(Not run)
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