WOLFRAM

Wolfram Language & System Documentation Center

NEXUS (.nex, .nxs)

  • Import can read sequence data and distance matrices from NEXUS files.
  • Export converts sequence data to the NEXUS format.

Background & Context

    • NEXUS phylogenetic file format.
    • Commonly used for storage and exchange of phylogenetic data.
    • Can store DNA and protein sequences, taxa distances, alignment scores, and phylogenetic trees.
    • ASCII format.
    • Allows user extensions.
    • Developed in the 1990s.

Import & Export

  • Import["file.nex"] imports DNA or protein sequences from a NEXUS file.
  • Export["file.nex",expr] exports a sequence or list of sequences to the NEXUS file.
  • Import["file.nex"] returns a list of strings representing the sequences stored in the file.
  • Export["file.nex",str] exports a character string representing a DNA or protein sequence to NEXUS.
  • Export["file.nex",{str1,str2,…}] exports multiple sequences.
  • Import["file.nex",elem] imports the specified element from a NEXUS file.
  • Import["file.nex",{"elem","sub",…}] imports a subelement.
  • Import["file.nex",{{elem1,elem2,…}}] imports multiple elements.
  • The import format can be specified with Import["file","NEXUS"] or Import["file",{"NEXUS",elem,…}].
  • Export["file.nex",expr,elem] creates a NEXUS file by treating expr as specifying element elem.
  • Export["file.nex",{expr1,expr2,…},{{elem1,elem2,…}}] treats each expri as specifying the corresponding elemi.
  • Export["file.nex",expr,opt1->val1,…] exports expr with the specified option elements taken to have the specified values.
  • Export["file.nex",{elem1->expr1,elem2->expr2,…},"Rules"] uses rules to specify the elements to be exported.
  • See the following reference pages for full general information:
  • Import, Exportimport from or export to a file
    CloudImport, CloudExportimport from or export to a cloud object
    ImportString, ExportStringimport from or export to a string
    ImportByteArray, ExportByteArrayimport from or export to a byte array

Import Elements

  • General Import elements:
  • "Elements" list of elements and options available in this file
    "Summary"summary of the file
    "Rules"list of rules for all available elements
  • Data representation elements:
  • "DistanceMatrix"distances between taxa given as a numerical matrix
    "Sequence"sequences given as a list of strings
    "Taxa"taxon names
  • Import uses the "Sequence" element by default.
  • Additional data elements:
  • "Data""Taxa" and "Sequence" elements combined in a list
    "LabeledData"list of rules for each taxon and sequence stored in the file
  • The Wolfram Language uses the standard IUB/IUPAC abbreviations for nucleic acids and amino acids. See the reference page for "FASTA" for detailed information.

Examples

Basic Examples  (6)

Import sequence data from a NEXUS file:

Import the taxon names and sequence data as a list of rules:

Export DNA sequences to the NEXUS format:

Export a pair of DNA sequences with explicit taxon names:

This returns the taxon names stored in the file along with a distance matrix:

Import taxon names and sequence data as pairs: