Writing alignments

Alignments can be saved in fasta, nexus, and phylip formats.

write_fasta(x, path)

write_nexus(x, path)

write_phylip(x, path)

Arguments

x

Alignment to save (an object of class DNAbin).

path

Path of the file to be written, without file extension (the appropriate extension is added automatically, i.e. the path will be extended with ".fasta", ".nexus", or ".phy" depending on the file format used).

Value

The input x (invisibly).

Examples

if (FALSE) {
  # Path to an example alignment file
  pkg_aln <- concatipede_example("COI_Macrobiotidae.fas")
  # Load the alignment into the R session
  aln <- ape::read.FASTA(pkg_aln)
  # Write the alignment in various formats
  # Note that the appropriate file extension is added by the writing functions.
  write_fasta(aln, "my-alignment")
  write_nexus(aln, "my-alignment")
  write_phylip(aln, "my-alignment")
}