read.nexus.data: Read Character Data In NEXUS Format

In ape: Analyses of Phylogenetics and Evolution

Read Character Data In NEXUS Format

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

read.nexus.data(file)
nexus2DNAbin(x)

Arguments

file	a file name specified by either a variable of mode character, or a double-quoted string.
x	an object output by read.nexus.data.

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):

• I: Comments 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!

• II: No spaces (or comments) are allowed in the sequences. Examples:
  name ACGT — OK
  name AC GT — NOT OK!

• III: No 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!

• IV: The 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!

• V: Multistate 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!

• VI: The number of taxa must be on the same line as ntax. The same applies to nchar. Examples:
  ntax = 12 — OK
  ntax =

  12 — NOT OK!

• VII: The 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

## Use read.nexus.data to read a file in NEXUS format into object x
## Not run: x <- read.nexus.data("file.nex")

ape documentation built on May 29, 2024, 10:50 a.m.