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Get aligned sequences from the Fish Tree of Life

Source: R/functions.R
fishtree_alignment.Rd

Retrieves an aligned sequence via the Fish Tree of Life API. If neither `species` nor `taxon` are specified, returns the entire sequence matrix.

Usage

fishtree_alignment(
  species,
  taxon,
  split = FALSE,
  release = getOption("fishtree.release", .default_release),
  rank = deprecated()
)

Arguments

species

(Optionally) subset the results based on a vector of species names.

taxon

(Optionally) subset the results to the taxon with this name, such as a family or order (e.g., `"Acanthuridae"`).

split

Splits the output into a list by gene locus.

release

The tree release to use, from fishtree_releases. Defaults to `getOption("fishtree.release")`, or `"R2018"` if that is unset. Looking up a `taxon` is only available for `"R2018"`.

rank

Deprecated; use `taxon` instead.

Value

An object of class `"DNAbin"`, or a named list of the same if `split = TRUE“

References

Rabosky, D. L., Chang, J., Title, P. O., Cowman, P. F., Sallan, L., Friedman, M., Kashner, K., Garilao, C., Near, T. J., Coll, M., Alfaro, M. E. (2018). An inverse latitudinal gradient in speciation rate for marine fishes. Nature, 559(7714), 392–395. doi:10.1038/s41586-018-0273-1

See also

DNAbin

Examples

if (FALSE) { # \dontrun{
surgeon_dna <- fishtree_alignment(taxon = "Acanthuridae", split = TRUE)
surgeon_dna[[1]]
par(mfrow = c(9, 3), mar = c(0.5, 0.5, 1, 0.5), xaxt = "n", yaxt = "n")
for (gene in names(surgeon_dna)) {
  image(surgeon_dna[[gene]], legend = FALSE, show.labels = FALSE)
  title(gene)
}
} # }