SOFTWARE FAQ's

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General issues

1. I am having problems formatting the sequences as nexus or phylip interleaved

   Try ALTER.

2. Why do I get strange files, that start with "." or "-" when I unzip these packages on Windows?

   These are macintosh hidden files, which can be safely removed without affecting the software. Note that unzipping with older MacOS (check whether you have the latest one) can also be problematic.

3. Do I need to register everytime I download any software, even if I subscribed before?

   Yes. It should not be too much work ... ;-)

4. The example files do not work in Windows ...

   It is very possible that you need to format these files for windows. This is easy to do. Just open them in Word Pad (or any other text editor) and save them with a different name. If you use Word, remember to save them in text format.

5. The program does not seem to be able to open some files in a Windows folder ...

   Maybe the extension of the file is hidden and you are typing the wrong name. Make sure that you know exacty the name of the file you want to open. Then, ckech that the format is that indicated in the documentation.

6. The source code is not included in the Java program distributions anymore, how can I obtain this code?

   You can unpack the java classes from the *.jar file using the "jar" program of the Java distribution. Then you can use a tool like "jad" (http://kpdus.tripod.com/jad.html) to decompile the classes into source code.

jModelTest

1. jModeltest cannot read the input alignment

   First make sure that the input file is in the same folder as the jModelTest folder, and that this folder is in path without "strange" symbols ("$%_ñ$!,space, etc"). Then transform the file for jModelTest using ALTER.

Modeltest

1. Modeltest says that the input file is incorrect, and that it has less models than expected ...

   First make sure that you are using the last modelblock file. If so, make sure that all the intendend models were included in the model.scores file. Check the PAUP web site for potential problems affecting the creation of the scores file.

2. I am having trouble running Modeltest on Windows

   Modeltest runs on Windows on a terminal window (MS-DOS), and this is why nothing happens when you double-click on it. Follow the instructions in the documentation. Also, Bevan Weir has put together a web page with detailed instructions for running Modeltest on Windows, and Paulo Nuin has written a windows interface for modeltest called MTgui.

3. The macintosh executable does not seem to work in my Macintosh

   There might be some incompatibilities between the latest Mac OS, and I do not have control over it. I always work with the latest MacOS. Make sure you have the latest MacOS

TCS

1. In the newer versions of TCS the "Cladograph Nesting" option is not available anymore ... why is this?

   That option was available in the past by mistake. It was not finished then and it is not finished now. We find very difficult to implement a nesting algorithm that works in any possible network, so right now we prefer that the user makes those decisions by designing the nesting by hand. The user is referred to examples in the literature.

2. I have problems when trying to print the network, or when exporting it as a postcript or PICT file

   The printing and exporting options do not work always well. To print you will need to have a postcript printer. The PICT file created is correct, although not of much quality, and it can usually be open in a variety of graphic applications. In MacOS X the simplest thing to do is to use the Grab tool (this is a default application in MacOS X located in the Utilities folder inside the Applications folder) to capture the network and produce a TIFF file. In Windows similar tools might exist. For publication purposes I always redraw the netowrk from scratch in a drawing program liek Canvas or Adobe Illustrator.

Collapse

1. In Windows, the program crashes and get a memory address problem

   This might occur when the input file is in mac format. Open the input file in WordPad and save it again, replacing the old one.

2. I have too many sequences, and in the terminal window cannot scroll up to see the complete output

   Redirect standard otuput to a file using: ./collapsex.x dataunix > outfile

3. How do I cite Collapse?

   There is no formal citation for Collapse. I normally do not cite it when I use it, because it performs a very simple task, but I guess you can just refer to the web page. Something like: Collapse x.x (available from http://darwin.uvigo.es)