write_aln {concatipede} | R Documentation |
Writing alignments
Description
Alignments can be saved in fasta
, nexus
, and phylip
formats.
Usage
write_fasta(x, path)
write_nexus(x, path)
write_phylip(x, path)
Arguments
x |
Alignment to save (an object of class |
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
## Not run:
# 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")
## End(Not run)
[Package concatipede version 1.0.1 Index]