read.nexus.data: Read Character Data In NEXUS Format
In gjuggler/ape: Analyses of Phylogenetics and Evolution

Description Usage Arguments Details Value Author(s) References See Also Examples

This function reads a file with sequences in the NEXUS format.

1	read.nexus.data(file)

file

a file name specified by either a variable of mode character, or a double-quoted string.

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

A list of sequences each made of a single vector of mode character where each element is a (phylogenetic) character state.

Johan Nylander nylander@scs.fsu.edu

Maddison, D. R., Swofford, D. L. and Maddison, W. P. (1997) NEXUS: an extensible file format for systematic information. Systematic Biology, 46, 590–621.

read.nexus, write.nexus, write.nexus.data