tree.raxml | R Documentation |
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.
tree.raxml(
folder = "2.Alignments",
FilePatterns = "Masked_",
raxml_exec = "raxmlHPC",
Bootstrap = 100,
outgroup,
partitioned = FALSE,
...
)
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 |
raxml_exec |
Where to find |
Bootstrap |
Number of bootstrap replicates (numeric). |
outgroup |
A single string of comma-separated tip labels to be
used as outgroup in |
partitioned |
Whether analyses should be partitioned by gene (Logical). |
... |
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"
)
## End(Not run)
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