Permission to use and distribute this software and its documentation for any purpose is hereby granted without fee, provided the above copyright notice, author statement and this permission notice appear in all copies of this software and related documentation.

THE SOFTWARE IS PROVIDED "AS-IS" AND WITHOUT WARRANTY OF ANY KIND, EXPRESS, IMPLIED OR OTHERWISE, INCLUDING WITHOUT LIMITATION, ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.IN NO EVENT SHALL THE AUTHOR, THE DIVISION OF ENVIRONMENAL AND EVOLUTIONARY BIOLOGY OR THE UNIVERSITY OF GLASGOW BE LIABLE FOR ANY SPECIAL, INCIDENTAL, INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND, OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER OR NOT ADVISED OF THE POSSIBILITY OF DAMAGE, AND ON ANY THEORY OF LIABILITY, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

Contents

• Taxon properties
• Adding a taxon
• Deleting and reordering taxa
• Finding a taxon

• Character properties
• Adding a character
• Deleting and reordering characters

• RTF reports
• HTML reports

• DELTA
• Hennig86
• Simple table

Introduction

In addition to a spreadsheet data editor, NDE makes it easy to fully annotate the data with both text and pictures, and to have lengthy descriptive character and character state names. This last feature avoids the constraint imposed by MacClade of character and state names being being limited to 32 characters. Hence cryptic phrases such as "ant. temp. marg." (anterior temporal margin) can be avoided. The ability to have lengthy character names, together with text comments, means that the data set can be largely self documenting. Indeed, if suitably constructed the character names and comments can be exported by the program directly into a file readable by a word processor, automating the production of character definitions for publication. NDE can also output HTML. Although designed as a NEXUS file editor, NDE also has limited support for other formats, including Hennig86 and DELTA.

Limitations

• Only supports "STANDARD" data type (i.e., does not support molecular data)
• Limit of 10 states per character
• Only supports ordered and unordered characters
• No character weighting
• No support for taxon sets
• No tree display or analysis functions

Incompatibilities with MacClade

Reading MacClade files in NDE

Token	Can be read by MacClade	Can be read by NDE
interval_4+5_micro.	yes	no
'interval 4+5 micro.'	yes	yes

NDE cannot read any pictures stored in the MacClade files. This is because MacClade stores the pictures in the resource fork of the file, and Windows files don't have resource forks.

Getting started

Downloading and installing the program

NDE requires a PC running Windows 95 or NT 4.0 or later. To install the program unzip the distribution file and run the program SETUP.EXE. You can delete NDE using the Add/Remove Programs control panel.

Please register!

• If you download the program please register it by sending me an email. This will ensure you are keep informed about bug fixes and new releases.

Creating a new data file

Opening existing data files

The spreadsheet window

The taxon names are shown in a column on the left; along the top of the spreadsheet are numbered columns representing the characters. When thecursor is moved over either the taxon names or character numbers it changes to a finger . Clicking the mouse will display the taxon (or character) properties dialog box with the corresponding taxon (character) selected.

When the cursor is over the data sheet the cursor is cross-shaped . Each cell contains a coded description of the attributes of a taxon for that character. Typically the attribute is a single character state. Clicking on a cell activates the data editor (see the section Entering data). It also updates the information displayed in the attributes panel below the spreadsheet.

Attributes panel

Taxa

Taxon properties

Adding new taxa

Deleting and reordering taxa

Deleting and reordering taxa is performed using the Manage taxa dialog box.

This dialog lists all the taxa in the matrix. If you select a single taxon you can click on the (up) and (down) buttons to change its order in the matrix. You can select one or more taxa for deletion by holding down the Shift key and clicking on the names of the taxa you wish to delete. Once you've selected the taxa, click on the Delete button to delete them.

Warning

• If you click on the Delete button the taxa are deleted from the list in the dialog box, but not from the data matrix. The taxa are only deleted once you press the Ok button. However, once you press Ok the deletion cannot be undone, hence delete taxa with care! If you press Cancel then no taxa will be deleted.

Finding a taxon

Select the desired taxon from the list and press OK. The selected taxon wil be highlighted.

Characters

Character properties

Character tab

The Character tab displays the full name of the character, which you can edit. You can also specify whether the character is ordered or unordered (these are currently the only two types of characters NDE supports).

States tab

The States tab lists the states for the character. Each state is listed with the corresponding code used in the data matrix. You can edit or delete the selected state, or add a new state.

If you delete a character state then the program will recode any taxon that had that character state as having missing data ("?") , unless the taxon is scored as polymorphic, in which case the taxon will be assigned the state(s) remaining after removing the deleted character state.

You can reorder the character states using the (up) and (down) buttons. Note that the order of the states is only relevant if the character is ordered.

Choosing to edit or add a character state displays a dialog box in which you can enter the state name, any notes, and a picture. See the section "Annotating your data" for more information.

Adding new characters

Deleting and reordering characters

Entering data

NDE will alow only certain symbols to be entered into a cell, namely the numbers '0'-'9' which correspond to the allowed character states, the symbols for missing '?' or inapplicable data '-', and '/' and '+'. These last two symbols are used to describe polymorphisms; '/' is equivalent to "or," and '+' is equivalent to "and". For example, scoring a taxon as "0/1" means it has either state 0 or state 1 for that character; "0+1" means that it has both states. Once a cell has been edited NDE displays its contents in boldface so that you know which cells you have edited.

NDE requires that any character state entered in a cell already exists. For example, if you have a character with two states, '0' and '1', and you attempt to enter '2' in the cell, the program will complain that '2' is not a valid state for the character. In order to enter '2' you must first add that state to the list of states for the character using the Character properties dialog box.

Warning

• NDE does not support undo, so edit your data with care. However, pressing the Esc key will exit the cell without the cell's contents being changed.

Moving between cells

Fast data entry using autotab

These two buttons determine whether the editor automatically moves to the right (i.e., the next character for the current taxon), or downwards (i.e., the next taxon for the current character). Note that in autotab mode you cannot enter more than one state for a taxon. To switch autotab off, simply click on the depressed button.

Attribute properties

Annotating your data

Adding text comments

You can use the comments to make notes about various data elements, such as "specimen missing left leg", or you can write detailed comments suitable for publication. NDE can export comments in a format readable by most word processors, so you do not have to duplicate the effort of commenting your data in both NDE and a manuscript. See below for more details.

Adding pictures

To associate a picture with a data element, click on the button and select the desired picture file.

Currently the NEXUS format supports pictures in encapsulated Postscript (EPS), GIF, JPEG, Macintosh PICT and TIFF formats. NDE stores the name of the picture file relative to the data file, such that given a data file c:\data\myfile.nex, the picture file c:\data\images\mypicture.jpeg is referred to as images\mypicture.jpeg. Because changing the location of a picture file with respect to the data file will break this link between data and picture, I suggest that you keep the images together in a folder within the folder that holds the data file (as in the example above where the folder images is nested within the folder data).

This means that if you move both the folder data (which contains both the data file and the image folder together) to a new location on your disk, the program will still be able to find the images.

NDE uses your Web browser (if installed) to display pictures. Clicking on the View picture button will launch the default browser (if it is not already running) and attempt to display the picture. If the picture format is not supported by the browser then you may need to use a helper application to view the image. For example, GIF and JPEG files can be viewed within your browser, but TIFF files will probably require an external viewer such as LView or Paintshop Pro, or a plugin.

Character sets

This dialog box displays the current character sets you have defined. You can Add, Delete, ename, or Edit these sets.

Merging data sets

Generating reports

Character reports for publication

NDE can create two alternative styles of character report, either a simple indented list with each character and character state on a new line, or an indented, numbered list of characters and states, together with any comments you may have written:

If you are using a bibliographic program such as EndNote, you can include citations to papers in the comments. These will be written in the RTF file, and hence included in your manuscript.

HTML reports

Any pictures you associate with your data are converted into hyperlinks in the HTML report. For example, if a taxon has a picture associated with it, then the name of that taxon is displayed as a hyperlink, and clicking on it displays the image in a separate popup window. Try it by clicking on this link to see an image of a beetle (this requires a Web browser that supports JavaScript, such as Netscape 2.0 or above).

Warning

• At present the HTML report generator assumes that the HTML file will be saved in the same folder as the data file, otherwise the links to any pictures will not work.

Other file formats

DELTA

Reading DELTA files

Warning

• The code to read DELTA files is in an VERY early stage of development, and is very slow and buggy. Do not expect much at this stage!

To import data in DELTA format, choose the Import | DELTA command on the File menu. NDE will display a dialog box sprompting you for the names of the CHARS, ITEMS, SPECS and (optionally) the CNOTES files. Click on the buttons to select the corresponding files. You will need to have selected at least the CHARS, ITEMS and SPECS files before the OK button is enabled.

If the DELTA files are successfully read the program will display the imported data in a spreadsheet window.

Writing DELTA files

When writing DELTA files, NDE writes any character comments to the CNOTES file (if specified); all other comments are written after the corresponding data element. Pictures are currently not exported.

Hennig86

Importing Hennig86/Tree Gardener files

Exporting Hennig86 files

To export in hennig86 format choose the File | Export | Hennig86 command. For information on using Hennig86 click here.

Simple table

             1 2 3 4 5 6 7 8 9 10 
californicus 0 0 1 1 0 1 0 0 0 0
centralis    0 0 1 1 0 1 0 0 0 0 

One use of simple text tables is to import them into a spreadsheet program (such as Excel) for printing. programs like Excel have much greater flexibility in formating and printing than does NDE.

Acknowledgments