fishtree_alignment: Get aligned sequences from the Fish Tree of Life
| fishtree_alignment | R Documentation |
Get aligned sequences from the Fish Tree of Life
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
fishtree_alignment(species, rank, split = FALSE)
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
## 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)
