read.nexus.data
reads a file with sequences in the NEXUS
format. nexus2DNAbin
is a helper function to convert the output
from the previous function into the class "DNAbin"
.
For the moment, only sequence data (DNA or protein) are supported.
read.nexus.data(file)
nexus2DNAbin(x)
a file name specified by either a variable of mode character, or a double-quoted string.
an object output by read.nexus.data
.
A list of sequences each made of a single vector of mode character where each element is a (phylogenetic) character state.
This parser tries to read data from a file written in a restricted NEXUS format (see examples below).
Please see files data.nex
and taxacharacters.nex
for
examples of formats that will work.
Some noticeable exceptions from the NEXUS standard (non-exhaustive list):
IComments must be either on separate lines or at the
end of lines. Examples:
[Comment]
--- OK
Taxon ACGTACG [Comment]
--- OK
[Comment line 1
Comment line 2]
--- NOT OK!
Tax[Comment]on ACG[Comment]T
--- NOT OK!
IINo spaces (or comments) are allowed in the
sequences. Examples:
name ACGT
--- OK
name AC GT
--- NOT OK!
IIINo spaces are allowed in taxon names, not even if
names are in single quotes. That is, single-quoted names are not
treated as such by the parser. Examples:
Genus_species
--- OK
'Genus_species'
--- OK
'Genus species'
--- NOT OK!
IVThe trailing end
that closes the
matrix
must be on a separate line. Examples:
taxon AACCGGT
end;
--- OK
taxon AACCGGT;
end;
--- OK
taxon AACCCGT; end;
--- NOT OK!
VMultistate characters are not allowed. That is,
NEXUS allows you to specify multiple character states at a
character position either as an uncertainty, (XY)
, or as an
actual appearance of multiple states, {XY}
. This is
information is not handled by the parser. Examples:
taxon 0011?110
--- OK
taxon 0011{01}110
--- NOT OK!
taxon 0011(01)110
--- NOT OK!
VIThe number of taxa must be on the same line as
ntax
. The same applies to nchar
. Examples:
ntax = 12
--- OK
ntax =
12
--- NOT OK!
VIIThe word “matrix” can not occur anywhere in
the file before the actual matrix
command, unless it is in
a comment. Examples:
BEGIN CHARACTERS;
TITLE 'Data in file "03a-cytochromeB.nex"';
DIMENSIONS NCHAR=382;
FORMAT DATATYPE=Protein GAP=- MISSING=?;
["This is The Matrix"]
--- OK
MATRIX
BEGIN CHARACTERS;
TITLE 'Matrix in file "03a-cytochromeB.nex"';
--- NOT OK!
DIMENSIONS NCHAR=382;
FORMAT DATATYPE=Protein GAP=- MISSING=?;
MATRIX
Maddison, D. R., Swofford, D. L. and Maddison, W. P. (1997) NEXUS: an extensible file format for systematic information. Systematic Biology, 46, 590--621.
# NOT RUN {
## Use read.nexus.data to read a file in NEXUS format into object x
# }
# NOT RUN {
x <- read.nexus.data("file.nex")
# }
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