write.dna(x, file, format = "interleaved", append = FALSE,
nbcol = 6, colsep = " ", colw = 10, indent = NULL,
blocksep = 1)read.dna and the references below for a description.If the sequences have no names, then they are given "1", "2", ... as names in the file.
With the interleaved and sequential formats, the sequences must be all of the same length. The names of the sequences are not truncated.
The argument indent specifies how the rows of nucleotides are
indented. In the interleaved and sequential formats, the rows with
the taxon names are never indented; the subsequent rows are indented
with 10 spaces by default (i.e., if indent = NULL). In the FASTA
format, the rows are not indented by default. This default behaviour
can be modified by specifying a value to indent: the rows are then
indented with ``indent'' (if it is a character) or `indent' spaces (if
it is a numeric). For example, specifying indent = "" or
indent = 3 will have the same effect (use indent = "\t"
for a tabulation).
The different options are intended to give flexibility in formatting the sequences. For instance, if the sequences are very long it may be judicious to remove all the spaces beween columns (colsep = ""), in the margins (indent = 0), and between the blocks (blocksep = 0) to produce a smaller file.
Anonymous. IUPAC ambiguity codes.
Felsenstein, J. (1993) Phylip (Phylogeny Inference Package) version
3.5c. Department of Genetics, University of Washington.
read.dna, read.GenBank,
makeLabel