Get aligned sequences from the Fish Tree of Life

Source: R/functions.R

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)

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

surgeon_dna <- fishtree_alignment(rank = "Acanthuridae", split = TRUE)
surgeon_dna[[1]]

#> 67 DNA sequences in binary format stored in a matrix.
#> 
#> All sequences of same length: 979 
#> 
#> Labels:
#> Acanthurus_achilles
#> Acanthurus_auranticavus
#> Acanthurus_bahianus
#> Acanthurus_bariene
#> Acanthurus_blochii
#> Acanthurus_chirurgus
#> ...
#> 
#> Base composition:
#>     a     c     g     t 
#> 0.302 0.258 0.220 0.220 
#> (Total: 65.59 kb)
if (FALSE) {
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)
}
}