NEXUS Data Editor for Windows
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NEXUS Data Editor for Windows

A program to edit NEXUS format data files

Roderic D. M. Page
(Last modified 1 February 1999)


Copyright 1999 Roderic D. M. Page.

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

  • Introduction
  • Limitations
  • Getting started
  • Taxa
  • Characters
  • Entering data
  • Annotating your data
  • Character sets
  • Merging data sets
  • Character reports for publications
  • Other file formats
  • Acknowledgments

  • Introduction

    NDE (NEXUS Data Editor) is a program to create and edit NEXUS format data files on computers running Microsoft Windows 95/NT 4.0. The main motivation behind my writing the program was to provide an easy to use data editor similar to that provided in the Macintosh program MacClade (note that NDE has none of the data or tree analysis features of MacClade). The NEXUS format is becoming more widely used on PCs now that DOS and Windows versions of PAUP* are available for testing.

    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

    NDE is in a very early stage of development, and there are numerous limitations, not all of which are mentioned here. In particular, the program will only handle nonmolecular data sets, such as morphology and behaviour. Molecular data typically poses a different set of problems (such as alignment), and rarely do individual molecular characters and states require detailed annotation. The progam recognises only subset of the NEXUS format, and has these limitations:

    Incompatibilities with MacClade

    Reading MacClade files in NDE

    MacClade is a little less strict in its adherence to the NEXUS standard than NDE, hence some files created in MacClade may cause errors in NDE. Look at the output in the Log window for any error messages. A common problem is that MacClade allows tokens (such as taxon and character names) to include symbols such as "+" (e.g., interval_4+5_micro.) whereas NDE does not. NDE will accept such symbols only if the token is enclosed in single quotes. For example:

    TokenCan be read by MacCladeCan be read by NDE
    interval_4+5_micro.yesno
    'interval 4+5 micro.'yesyes

    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

    Download NDE from http://taxonomy.zoology.gla.ac.uk/rod/NDE/nde.html

    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!

    Creating a new data file

    To create a new data file choose the File | New command. NDE will create a data matrix with three taxa and one character.

    Opening existing data files

    You can open NEXUS files within NDE using the File | Open command. You can also open document files with the extension .nex by right-clicking on the document and choosing the Edit in NDE command on the popup menu:

    The spreadsheet window

    NDE displays the data in a 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

    This panel displays the character name and states for the current character, with the states represented by the codes in the cell highlighted in boldface. You can resize this panel by moving the mouse over the horizonatl bar separating the panel from the spreadsheet. The cursor will change to a vertical resize cursor enabling you to alter the size of the panel.


    Taxa

    Taxon properties

    The Taxon Properties dialog box is displayed whenever the user clicks on a taxon name with the cursor , or if the Data | Taxon properties command is chosen. The dialog box displays a list of all the taxa on the left, and on the right are edit boxes for the taxon name and comments, and controls to add a picture.

    Adding new taxa

    One or more new taxa can be added using the Add taxa command. In the resulting dialog box simply type in the number of taxa to create. These will be added to the bottom of the data sheet with all their attributes set to missing data ("?").

    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

    Finding a taxon

    If the data sheet is larger than the size of your screen, the taxon of interest might not be visible. The Goto taxon command enables you to scroll to the desired taxon.

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


    Characters

    Character properties

    The Character Properties dialog box is displayed whenever the user clicks on a character number with the , or if the Data | Character properties command is chosen. The dialog box displays a list of all the characters on the left, and on the right are four tabs displaying properties of the currently selected character.

    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

    One or more new characters can be added using the New characters command. In the resulting dialog box simply type in the number of characters to create. These will be added to the right of the data sheet, and each taxon will be scored as missing ("?") for this character.

    Deleting and reordering characters

    Deleting and reordering characters is performed using the Manage characters dialog box. This dialog box is vitrually identical to the Manage taxa dialog box.


    Entering data

    To enter or edit a cell in the spreadsheet simply click on that cell. The cell's contents are highlighted and can be edited, and the cursor changes to the edit cursor . The corresponding taxon name and character number are also highlighted in boldface. In the example below, the attributes of taxon albati for character 2 are being edited.

    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

    Moving between cells

    When editing a cell you can move to adjacent cells using either the arrow keys, or the tab key.

    Fast data entry using autotab

    NDE's autotab feature enables you to enter data and move between cells at the same time. After typing a single symbol the editor moves to the next cell. Autotabbing is enbabled by depressing either of the two autotab buttons on the tool bar.

    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

    If a cell is selected the Attribute properties button on the tool bar is enabled. Clicking this button displays the Attribute properties dialog box, in which you can add comments on the contents of the cell (for example, whether the information is based on your observatons or from the literature), and add a picture (for example, an SEM of the character in this taxon). The Notes and Picture tabs display any comments and picture associated with the observations for this taxon and character. See the section "Annotating your data" for more information.

    Annotating your data

    Within NDE you can add text comments and pictures to any data element, including taxa, characters, character states, and taxon attributes.

    Adding text comments

    To add comments simply type text in the edit box. You can type up to 2048 characters. You can include bibliographic citations, such as those produced by EndNote (e.g., [Bartschwinkler, 1988 #20]) to document your data.

    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

    Although the NEXUS format supports pictures being stored as separate files, in the resource fork of Macintosh files, or "inline" as a string of ASCII characters, NDE only implements the first option (separate image files).

    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

    Character sets are useful tools for grouping related characters together, such as those from the same sex or developmental stage. When analysing your data in PAUP you can use characetr sets to select subsets of your characters for phylogenetic analysis. If you choose the Sets | Characters menu you will see this dialog box:

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


    Merging data sets

    NDE can merge two NEXUS format files, providing that the files have the identical taxa in them. For example, you may have two data sets for the same taxa that represent different parts of the body of your study organism (e.g., head and torso). Using the File|Merge command you can join these two data sets together.

    Generating reports

    NDE can generate reports in RTF and HTML formats. This feature makes it easy to incoporate character descriptions in manuscripts, and to provide colleages ready access to your data even if they lack a NEXUS data editor such as NDE or MacClade.

    Character reports for publication

    NDE can create a formatted list of characters and character states for inclusion in a manuscript for publication. This feature is designed so that you need describe the chacters and their states only once (within NDE). Rather than retype this information in your manuscript, you can use the Character report command to produce a Rich Text Format (RTF) file which can be read by most word processors (such as Microsoft Word, WordPerfect, etc.) as well as the WordPad accessory that comes with Windows 95.

    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

    NDE can create an HTML report of the data set for viewing in a Web browser. This provides a convenient way for you (or others) to view the data and associated notes and pictures.

    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


    Other file formats

    DELTA

    NDE has limited support for reading and writing DELTA format files. DELTA (DEsciptive Language for TAxonomy) is designed to enable taxonomists to store information about taxa in a form that can be readily converted to natural language descriptions and taxonomic keys. As such its goal is somewhat different from the NEXUS format, although the two systems overlap to some extent.

    Reading DELTA files

    Warning

    NDE recognises a limited subset of the DELTA format. Whereas DELTA allows five different types of character: ordered (OM) and unordered (UM) mult istate, integer (IN) and real (RN) numbers, and text (TE) characters, NDE will import only OM and UM characters. Currently NDE cannot handle implicit character states, nor does it recognise dependent characters. DELTA is also less structured than NEXUS, so that comments can be inserted in almost any part of a data element description. Because of this, NDE will ignore some comments. (to do: discuss this in more detail).

    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

    NDE can write CHARS, ITEMS, SPECS, and (optionally) CNOTES files. To export data in DELTA format, choose the Export | 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 specify the corresponding files. I recommend that you use the default names for these files ("chars", "items", "specs", and "cnotes", respectively). You may also find it useful to save the DELTA files in a separate folder within your data folder. Note that you will need to have specified at least the CHARS, ITEMS and SPECS files before the OK button is enabled.

    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

    NDE can import Hennig86 files. Currently NDE will read the data matrix but not the ccode command (which specifies whether the characters are ordered or unordered). NDE will also import files created using Tree Gardener. This program produces Hennig86-style files (with the extension *.mtr) that also contain the names of the characters and their states. NDE will read and store these names.

    Exporting Hennig86 files

    NDE can export your data in Hennig86 format. If a taxon is polymorphic for a character, NDE replaces the polymorphism by a "?". NDE will include a ccode command specifying the character types.

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


    Simple table

    NDE can export your data as a simple table. If you choose the File | Export | Simple table command you will be prompted for a file name. Once you've specified where you want the tabel saved, NDE displays the following dialog box:


    You can specify whether NDE uses the tab character or a space to separate the characters, and whether you want to include a row of character names in the table. A table might look something like this:

                 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

    Vince Smith's struggle to find a half way decent program to enter, store and manipulate phylogenetic data on a PC provided the initial incentive to write the program. NDE's debt to the Maddison's wonderful program MacClade is obvious. I also thank David Maddison for providing drafts of Maddison et al.'s description of the NEXUS format. Mario Calvacanti kindly made his DELTA Library code available. I also made use of Leo Breebaart's description of Microsoft's RTF format, and Smaller Animals Software's ImgDLL library for displaying images. NDE is written in C++ and compiled using Borland C++ 5.01 compiler.