Phenex

From phenoscape
Revision as of 19:46, 15 August 2008 by Jpb15 (talk | contribs)

Importing matrix files and taxon lists into Phenex

  1. In order to combine a taxon list created in Phenote with matrix data stored in a NEXUS file, both files need to use identical taxon names. For the Phenote file, this is the value in "Publication Taxon" (NOT "Valid Name"). For the NEXUS file, this is the ordinary taxon name you can see and edit in Mesquite. It is much easier if all the taxon names are made identical before you do the merge.
  2. First, open the taxon list in Phenote and the NEXUS file in Mesquite. Make sure all the taxon names you want to match are identical. It is okay if the files don't have the same number of taxa - if there are more in the taxon list, the extra taxa will be added. If there are fewer, you will just have some that don't get matched.
  3. While the NEXUS file is open in Mesquite, choose "File > Save File As..." and save a new copy of the NEXUS file. This will ensure that Mesquite re-writes the NEXUS file using a modern format which is more likely to be successfully opened by Phenex. Use this new copy of the NEXUS file for all subsequent steps.
  4. Launch Phenex. Choose "File > Import NEXUS...". Select your NEXUS file and open it. Verify that all the data is imported as expected, including the matrix.
  5. Now choose "File > Merge > Tab-delimited Taxa...". Select your taxon list file and open it. The import will seem a little slow. Verify that the taxa you loaded from your NEXUS file now have TTO terms associated with them in "Valid Name", and specimens in the specimens panel (assuming you had this data in your taxon list).
  6. If some taxa from the Phenote taxon list were not matched to existing taxa in Phenex, you will see them at the end of the list. Also, these taxa should have only empty cell values in the matrix panel. If you expected these taxa to match existing taxa, check the taxon names and start over.
  7. Save your Phenex data to a new file using "File > Save". It is recommended to append ".xml" to the file name.