Intro

Malin is a software package for the analysis of eukaryotic gene structure evolution. It provides a graphical user interface for various tasks commonly used to infer the evolution of exon-intron structure in protein-coding orthologs. The implemented tasks include the following.

Related stuff

My other related computer programs (including a program for multiple alignment of intron-annotated protein sequences) and information is accessible through my research page on intron evolution.

Liran Carmel wrote a spiffy software package called EREM (Evolutionary Reconstruction by Expectation-Maximization), which implements his results on analyzing gene structure evolution. See his webpage about it.

Availability

Malin is written entirely in Java, and, thus, can be used in different operating systems, including Mac OS X, Microsoft Windows, and various Unix/Linux versions. The software is packaged in a JAR file, and can be executed in Java versions 1.5 and above. The distributed platform-specific packages, described below, include the JAR file with the necessary bundling for execution, as well as the User's Guide and a test directory.

Version history

Mac OS X

I have written the software using a Mac, and went to some extent to integrate the Java executable into a native-looking application. The JAR file is bundled as Malin.app, which you can just run directly by double-clicking on it. Please note that the application attempts to set the memory usage for the Java Virtual Machine by enabling a maximum heap size of 1000 Megabytes. If your computer does not have that much memory (i.e., at least 1G), the application may not function properly. One solution is to follow the instructions for Unix/Linux below, and launch Malin from a Terminal window. Alternatively, you can send me an e-mail and I will gladly prepare a small-memory version of the application for you.

Installation: Download the disk image Malin.dmg, open it, and place the application Malin.app into an appropriate directory. For convenience, you may want to copy it to the Applications folder, either at the system level, or in your own home directory.

Microsoft Windows

You need to have a Java Virtual Machine on your computer in order to run Malin. You could download, for instance, Sun's Java Runtime Environment from http://www.java.com/, which is the JRE I used in the testing. You will probably need to enable larger memory usage for the JVM than the default setting, which you get by double-clicking on the JAR file. You can launch Malin via the provided MS-DOS batch file that sets the heap space for the JVM to 1000 Megabytes. Edit the batch file manually, if necessary.

Installation: Download the ZIP file Malin.zip. The archive contains the JAR file Malin.jar and the batch file Malin.bat.

Unix/Linux

You can launch Malin from the command line, by the command java -jar Malin.jar. You will probably need to enable larger memory usage for the JVM than the default setting, which you can do by launching Malin as java -Xmx1024M -jar Malin.jar. The -Xmx option here sets the Java heap space to 1 Gigabytes: you can experiment with other settings appropriate for your computer and data set.

Installation: Download the gzipped TAR file Malin.tgz into an appropriate directory. You can extract the files from the archive with the command tar -zxf Malin.tgz.

User's Guide

The User's Guide is available in PDF format as malin_guide.pdf. Relevant information is available also through the Help menu of the software package.

Licensing

Malin is distributed under the terms of a BSD-style license, as shown below

Copyright © 2008, Miklós Csűrös

All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

  1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
  2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
  3. Neither the name of the Université de Montréal nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS AS IS AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

I would be very grateful if you could send me a note in case you decide to use Malin. (Aside from making me happy, you'd have my promise of notifying you about future updates.)

Screen shots

Alignment panel Alignment panel screenshot

Rates panel Rates panel screenshot

Site histories Site histories screenshot

Bootstrapping Bootstrapping screenshot