Mesquite

Introduction
Why?
How to Cite
Publication
Support
Credits

Help
FAQ
Web Site

Simplicity
Files

Menus
Windows
Charts
Scripts/Macros
Modules
How

Characters
Taxa
Trees
Glossary

New
  Features

     

Table of
    Contents

 

Character
  Evolution

Diversification

Molecular
  Data

Gene trees

Simulations &
  Randomizations

Continuous
  Characters

Use with
  Other Programs

Studies

 
     

Support & Advice

If you think you've found a bug in Mesquite, our would like to suggest a feature, please read this page. For help in using Mesquite, see the Help page.

Why doesn't Mesquite do <insert your favorite calculation here>?

Mesquite is extensible. What it can do now is a small part of what we envisage. We're aware of many things that could be added. The biggest needs we feel at the moment are for likelihood calculations and more tools for examining character correlations.

We would welcome your suggestions at .

Of course, if you really want a new feature sooner than we can add it, you are welcome to write your own module to implement the feature. Contact us at or see the Mesquite website for information on development.

Why does <insert feature> not seem to work properly?

If you think you have found a bug in Mesquite, please report it to us (see below). If we don't know about a bug, it is unlikely that it will be fixed. It might be natural to presume that we know about all the bugs in Mesquite, but it is not possible for us to have tried out every combination of options on every computer environment with every data matrix, model, etc. If you are not sure if it is a bug (a large number of users blame themselves when they encounter a bug, presuming it is something they have done wrong), please report it anyway. Even if your apparent "bug" is a mistake you made, your mistake might indicate a poorly designed interface that should be corrected.

That there will be bugs in Mesquite is inevitable. Mesquite is a large project, about 1500 pages of source code when printed single spaced at 7 point font (about 120,000 or more lines of source; over 5MB of ASCII text). We don't have a big team of people working on it; it was initially written by a single person, and now most of it is written by only two people. We apologize for the bugs that remain, and look forward to your bug reports and efforts to aid us make Mesquite useful.

Mesquite is intended to become a community effort. Source code is available at the Mesquite web site; we hope other programmers will help us improve the system.

 

Check out the Help system first

Mesquite doesn't have conventional documentation for all of its features, but it does have various features to help you learn how to use it. Check out the help page for instructions. Also, browse through the example files, as they contain many explanations and hints.

We recognize that Mesquite is a complex system that offers many choices to the user. We plan to build macros and other tools to help build paradigmatic analyses for users who don't want to sort their way through options every time. However, they're only beginning to be built.

Reporting bugs and requesting advice

Please report bugs to . Some bugs you may encounter will be bugs not in Mesquite but in the operating system or Java virtual machine (for example, see this list).

Partly to foster a community of users, and partly for efficiency, we are encouraging users to sign up to a Mesquite mailing list via which they can post queries about using Mesquite. Once you've signed up, you can send a message to the list.

If you're reporting a bug, it's important that you are able to specify, as precisely as possible, exactly what you did that generated the bug. Try to find a precisely repeatable series of actions that generate the bug. In any bug report, please specify the version of Mesquite and any important modules and your operating system. Be prepared to send us your data file so we can test the problem. It is also very helpful to send us the Mesquite_Log file that is in Mesquite_Support_Files (which is in your home directory in Mac OS X and in "Documents and Settings\yourUserName\" in Windows). We need a copy of the log file as it was written immediately after your problem occurs.

(Of course, we recognize that some messages may be more appropriately directed directly to us. You may contact us at .

Java bugs that affect Mesquite

Below are problems in Java on various operating systems that affect Mesquite. If these problems annoy you, please contact those responsible for your Java virtual machine.


MacOS X

The recommended configuration for Mesquite on Mac OS X is OS X 10.5 with the latest Java. There are various screen redraw and crashing bugs in earlier versions of OS X and Java.

If at any point Mesquite quits spontaneously and OS X puts up a dialog that says that Mesquite has unexpectedly quit, this is what is called a "JVM crash". Technically it is not supposed to be possible for Mesquite to do this, and thus it represents a bug in Java and not a bug in Mesquite. Nonetheless, we would like to know about it, because we may be able to find a way to avoid the JVM bug.

MacOS X running Java 1.3.1

Mesquite 2 does not run under Java 1.3 or earlier.

MacOS X 10.0 through 10.2

We have not tested Mesquite 2 under these earlier versions of MacOS X.

Mac OS 9

Mesquite 2 does not function on Mac OS 9, because it requires Java 1.4.


Windows

  • Windows bounce up and down as menus change (a rapid shrink & expansion). This is due to a design flaw either in Windows or the Java VM; there is nothing we can do about it.
  • When you try to start Mesquite, you get a message that says it can't find Java. The JAVA_HOME may not be set properly on your machine To set it, go to System Properties (right click on My Computer and select Properties); Advanced tab; Environment Variables; look for Java_Home in the System variables window and edit it so that it points to the correct location of the latest Java installation.

Linux/Unix etc

  • Window sizes and placements sometimes are inappropriate under some window managers. Some window managers refuse to let Mesquite have control over window size and placement, and choose what appear to be random sizes and placements of windows. This is not in our control. Try changing your window manager. We have found that the default installations for KDE and Gnome of Red Hat 7 work well with Mesquite.
  • Messages about Fonts not found on startup may be given. The problem is that you need to install a supposedly optional package of fonts in order that the default installation of Sun's Java VM work properly (see http://java.sun.com/products/jdk/1.2/changes.html#sunw). We would have thought that if the default installation of a product claims to support a program but doesn't, then that would be considered a bug. Sun considered this to be not a bug, although they seem to have fixed it...


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Copyright © 2002-2009 by Wayne P. Maddison and David R. Maddison.
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