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

fishtree_alignment(species, rank, split = FALSE)



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


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


Splits the output into a list by gene locus.


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


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


if (FALSE) { 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) } }