write.dna(x, file, format = "interleaved", append = FALSE,
nbcol = 6, colsep = " ", colw = 10, indent = NULL,
blocksep = 1)read.dna: see its help page and the references below for
a description of these formats.
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; if the taxon names are longer than 10 characters,
they are truncated and a warning message is issued.
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 exactly the same effect (use `indent = "
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