Nexus Mode

The Nexus Illustrator is designed to illustrate taxa, characters, and character states in a standard nexus file. It also includes options to aid in the identification of the included taxa. In the standard view, which is the default Nexus Mode that is shown below, the taxon names are on the left hand column, the character and character state names are presented in top row, and the internal cells of the matrix contain illustrations of the character states for each taxon. The example shown below (Fig. 2) has about 49 species of Alabagrus (Hymenoptera: Braconidae: Agathidinae) and 871 high resolution jpeg images. There are only a small handful of "characters" presented to show how a Nexus file may be illustrated. The corresponding Nexus file is presented below (Fig. 1) immediately above the Nexus Illustrator (Fig. 2). These two files interact dynamically such that when changes in coding are made in the Nexus file they appear in Nexus Illustrator as well. The HymATOL project is currently looking at this software as our method of illustrating, or virtually vouchering, our morphological matrix for the skeletal, or core taxa, for our study of the phylogeny of the Hymenoptera.

If you go to the URL you can follow the steps below to view some of the characteristics of the Nexus Illustrator

• Step 1. If a taxon (left column) is selected, by left clicking once, all 17 standard images for that taxon are illustrated. For the HymATOL project we will include here a link to a homepage for the taxon which will contain much more information.
• Step 2. If a character is selected (top row), by left clicking once, example illustrations of the character states are presented. For the HymATOL project we intend to include here discussions on any character coding problems that are relevant to the character.
• Step 3. If any of the cells in the matrix are selected a high definition image appears.
• Step 4. If you left-click on the blue Nexus File Options box you are given the following options. Images; state numbers; state names; images and numbers, images and names. Click on these options to get different views of the Illustrated Nexus file.

Soon we expect to integrate this initiative with MorphBank which is being developed at Florida State University by Fredrik Ronquist and colleagues , such that the images will be deposited in Morphbank and Nexus Illustrator would interact dynamically with MorphBank data.

Screenshots


Figure 1: Nexus file for 49 species of Alabagrus and four characters.






Figure 2: Screen shot of a portion of the Nexus Illustrator corresponding to the Nexus file in Figure 1. The URL for this.