fishtree_alignment: Get aligned sequences from the Fish Tree of Life

Description Usage Arguments Value References See Also Examples

View source: R/functions.R

Description

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

Usage

1

Arguments

species

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

rank

(Optionally) subset the results based on the supplied taxonomic rank.

split

Splits the output into a list by gene locus.

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

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## Not run: 
surgeon_dna <- fishtree_alignment(rank = "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)
}

## End(Not run)

fishtree documentation built on Jan. 31, 2021, 1:06 a.m.