Description

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.

Usage

Arguments

Details

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

Value

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

Author(s)

Johan Nylander, Thomas Guillerme, and Klaus Schliep

References

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

See Also

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

Examples