AntMap: Software for Constructing Genetic Linkage Maps using an Ant Colony
Optimization Algorithm
Our paper reporting our algorithm and the software AntMap can be downloaded
from here!
Locus ordering is an essential procedure in genome mapping. When the number
of loci is large, it is quite difficult to determine the optimum order.
The problem of searching for the optimum order has been recognized as a
special case of the traveling salesman problem (TSP). In recent years, Ant Colony Optimization (ACO), which is a methodology inspired by the behavior of real ant colonies,
has been successfully used to solve TSP. We developed a novel system based
on ACO for locus ordering against such a background. We tested the system
using a simulated segregation population, and found it is highly efficient
for linkage mapping.
To commoditize our newly-developed system, we developed software named
AntMap for constructing linkage map by the system. AntMap performs segregation
test, linkage grouping and locus ordering, and constructs a linkage map
quite rapidly and nearly automatically. With the aid of this software,
researchers can save their time and labor, and can obtain a linkage map
whose reliability is indicated by bootstrap values.
For details about our algorithm and the software AntMap, please see Iwata and Ninomiya (2006).
Source code and executables of AntMap are available under GNU General Public License (GPL). Java classes that code our newly-developed system can be utilized effectively
for other applications as well as AntMap.
Executables, source code, and user's guide of AntMap can be downloaded
from the following link.
Version 1.2
| File Name |
Description |
Release Date |
| AntMap.zip |
Zip file which contains all files related to AntMap. |
2006/06/13 |
| AntMapSource.jar |
Java archive which contains Java source codes of AntMap |
2006/06/13 |
| AntMapDoc.jar |
Java archive which contains Javadocs of AntMap |
2006/06/13 |
| Manual.swf |
User's guide (FLASHPAPER version) |
2006/06/13 |
| Manual.pdf |
User's guide (PDF version) |
2006/06/13 |
Version 1.1
| File Name |
Description |
Release Date |
| AntMap.zip |
Zip file which contains all files related to AntMap. |
2005/05/18 |
| AntMapSource.jar |
Java archive which contains the source code of AntMap |
2005/05/18 |
| Manual.swf |
User's guide (FLASHPAPER version) |
2005/05/18 |
| Manual.pdf |
User's guide (PDF version) |
2005/05/18 |
The following systems are required for executing AntMap.
- Windows, Linux, Solaris or Mac OS.
- Java 2 Platform Standard Edition (J2SE) Java Runtime Environment (JRE)
(ver. 1.4 or higher).
If you have no J2SE JRE (ver. 1.4 or higher) already installed on your system, you should install the JRE to execute AntMap on your system. To install JRE, please see http://java.sun.com/javase/downloads/index.html.
AntMap can be easily installed to your system in the following steps.
- Download the zipped file named “AntMap.zip”, which contains all the AntMap files.
- Extract the folder named "AntMap" from “AntMap.zip”
- You can put the extracted folder anywhere you want.
The following short tutorial gives you instructions on how to try out AntMap
with sample data. Through this tutorial, you may become familiar with AntMap.
The tutorial is correspond to the current version (Ver.1.2).
The following links may be useful for your research.
Iwata H, Ninomiya S (2006) AntMap: constructing genetic linkage maps using
an ant colony optimization algorithm. 56: 371-377. <Abstract> <PDF>
Web site responsible: Hiroyoshi Iwata
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