Load the DNA sequences used to build the Fern Tree of Life (FTOL)

For details about the data, see plastome_alignment for plastome sequences and sanger_alignment for Sanger sequences.

Usage

ft_seqs(
  loci = NULL,
  plastome = FALSE,
  aligned = TRUE,
  del_gaps = ifelse(is.null(loci), FALSE, TRUE),
  drop_og = FALSE
)

Arguments

loci: Character vector (optional); names of loci to include in the output. If NULL (default), all loci will be included. For a list of valid locus names, see plastome_parts for plastome loci and sanger_parts for Sanger loci.
plastome: Logical vector of length 1; If TRUE, the alignment will include loci and species with complete plastomes available; otherwise will include Sanger loci and all species. Default FALSE.
aligned: Logical vector of length 1; If TRUE, the output will be aligned sequences (matrix); otherwise will be unaligned (list). Default TRUE.
del_gaps: Logical vector of length 1; If TRUE, all gaps will be deleted from the alignment. Default is TRUE if loci is NULL, FALSE otherwise.
drop_og: Logical vector of length 1; If TRUE, the outgroup (non-ferns) will be excluded; otherwise the outgroup is included. Default FALSE.

Value

List or matrix of class "DNAbin"; DNA sequences.

Details

After subsetting loci, columns / rows consisting of only gaps will be deleted regardless of del_gaps argument (del_gaps deletes all gaps, typically resulting in unaligned sequences).

For details on methods used to assemble alignments, see Nitta et al. 2022.

References

Nitta JH, Schuettpelz E, Ramírez-Barahona S, Iwasaki W. (2022) An open and continuously updated fern tree of life. https://doi.org/10.3389/fpls.2022.909768

Examples

# Default is aligned Sanger sequences
ft_seqs()
#> 5869 DNA sequences in binary format stored in a matrix.
#> 
#> All sequences of same length: 13384 
#> 
#> Labels:
#> Acrostichum_danaeifolium
#> Actiniopteris_dimorpha
#> Actiniopteris_semiflabellata
#> Adenophorus_sarmentosus
#> Adenophorus_tenellus
#> Adiantopsis_alata
#> ...
#> 
#> More than 10 million bases: not printing base composition.
#> (Total: 78.55 Mb)