What's new?

We will post here news about QGene updates.

Current version is: 4.4.0.

Key to release numbering

The first number (here, 4) describes the base feature package.
If we add features, we kick up the second number: 4.5.
If we fix bugs in 4.5, we tack on a third number: 4.5.1. This lets us fix unlimited bugs in 4.5 without reaching 4.6.
If we add important functionality we're ready to move up to version 5.0.


10.23.16 QGene is now distributed as a runnable (double-clickable) .jar file. Version 4.4.0 is compiled under Java 1.8_112, the latest release. A few bugs have been fixed, but the permutation-overrun bug that appears when 1000 iterations are selected has not. It is a threading (parallel-processing) error that I have not yet identified.

This version will run under Windows but not under OS X versions running recent Java releases. I hope to update it for OS X but can't give a due date.

8.3.16 Users have reported that QGene isn't running under Java 1.8 on either Windows or Macs — no one has said anything about Linux. I've restarted development and will release updated versions for these platforms when problems with the QGene launcher have been resolved.

5.28.15 Several users have reported that QGene won't run on OS X with Java 1.8x. The good news is that this failure could probably be remedied without much change to the source code. The bad news is that the only remaining developer (me) doesn't have a Mac and isn't maintaining QGene these days. Unless someone else wants to pick up the source code and solve the problem, Mac users' only option appears to be to stick with earlier versions of Java for OS X.

9.11.12 A 64-bit launcher has been provided by developer R. Joehanes and is included in the 4.3.10 distribution. In 64-bit Windows installations, use qgene64.exe as your double-clickable launcher (for most convenience, add it to your Startup menu as a shortcut).

Be sure that only the 64-bit JDK is installed; the presence of a 32-bit Java component can prevent launching.

This update should remove the necessity of using the command line as described below.

7.15.12 I've received several reports that QGene won't run on my Windows 7 machine.
In fact it WILL run. What won't work is the qgene.exe launcher.
So don't expect to double-click on qgene.exe any more, if you're using Windows 7.
Instead, open a console (or command-line) window and navigate to your QGene directory. Then enter


and QGene should start after you press the Enter key.

I'm sorry about the necessity for this workaround, but this launcher has always given more problems than the program itself. If someone would like to write one I doubt it would be hard to do. The QGene shop has only one developer these days (me), and he's otherwise occupied.

9.29.11 Version 4.3.10 is released with this fix:

  • Failure of ICIM module to account for cofactors for populations with dominant effects has been fixed.

8.12.11 Recent problems with WWW host

  • Coding, the machine hosting our QGene site, has been offline since 1 August, owing apparently to a defective memory module, but now seems to be running again.

6.6.11 Version 4.3.9 had an extra library

  • If you find you can't run CIM in QGene 4.3.9, find the "lib" directory of your installation and delete the file "jama.jar". It was included by mistake and has now been removed from the 4.3.9 distribution. Thanks to SS for reporting.

5.31.11 Version 4.3.9 is released with this fix:

  • The population simulator was ignoring the analyst's choices for missing data and dominant markers. I find this bug in versions at least as far back as 4.3.0, so either the feature is rarely used or its failure hasn't been noticed. Thanks to XW for reporting the problem.

10.21.10 No new release, but this correction made to the manual on the Data format page: in the genotype-symbol string of your QGene header, the recurrent parent in a backcross design should be represented by the first, not the second, symbol. This is the Mapmaker convention used in other programs.

10.4.10 Version 4.3.8 is released with these fixes:

  • Deadlocks on high-end multiprocessor machines have been fixed. Thanks to JC for reporting the problem.
  • Trait-regression-dialog bugs have been fixed.

8.10.10 Version 4.3.7 is released with these fixes and features:

  • A generalized R2 statistic is now available for all QTL methods, including multivariate and GLZ methods.
  • Trait regression dialog in trait analysis has been remodeled to show trait effects, p-values, and ANOVA tables. It also allows categorical and ordinal traits as independent and dependent variables.
  • Threading issues that caused permutation count to stick have been fixed.
  • Better support for modern CPUs with many cores has been added.
  • Missing OK button in auto fill trait simulation window has been fixed.
  • File qgene.bat for 64-bit Windows has been included again. It was missing in the 4.3.6 release.
  • Miscellaneous rarely encountered bugs have been fixed.

5.8.10 Version 4.3.6 is released with this fix:

  • Permutation analysis of SIM produced excessively high LOD score threshold in presence of dominance effect.

5.6.10 Version 4.3.5 is released with these fixes and features:

  • Division-by-zero bug described below has been fixed.
  • The aggressive memory allocation under Windows 32-bit introduced in version 4.3.4 has been toned down. QGene version 4.3.4 tried to allocate 1,583 Mb (the maximum amount allowed by 32-bit JDK) of memory whenever it could. This may fail in older machines.
  • From this version onwards, users with 64-bit OS should use 64-bit JDK version 1.6 or above to avoid memory allocation problems.

5.5.10 Version 4.3.4 has a division-by-zero bug in designs where dominance may be present. Permutations will give meaningless results and some analyses such as CIM will cause crashes. A fix will be applied in the next release.

4.15.10 A few users may have downloaded a 4.3.4 release that was packaged with an obsolete copy of file jama.jar in the lib directory. This causes CIM to fail. If you experience this problem, just delete that file and the error will disappear. The current download package no longer contains jama.jar and will not produce this error.

4.13.10 Version 4.3.4 is released with these fixes and features:

  • The MIM chatter described below has been fixed.
  • Computational instability of previous releases is fixed. One consequence was crashing during permutation analysis.
  • Linux and Mac OS X launcher scripts have been improved with memory autodetection.
  • On-the-fly memory status reporting is implemented. This allows real-time monitoring of memory use. It won't be needed unless you are working with a massive data set. Ordinary users -- forget it.
  • The manual has been updated to explain QGene's cofactor selection and clarify other points.
  • A subtle bug in chromosome scaling has been fixed. It took us a while to notice it (and probably no one else has), but the drawing scale of each chromosome was being dictated by the position label of its first marker. If that was always 0.0 cM the scales were uniform; otherwise not.
2.19.10 Version 4.3.3 is released with these fixes, features, and known bugs:
  • Various crashes in MLE and MIM methods (due to mishandled collinearity in partial regression) fixed.
  • Many Mac OS X bugs (file saving, permutation, etc.) fixed.
  • In QTL main contour window, additive-effect contour has been moved closer to LOD contour and scaled up.
  • Various other crashes fixed.
  • 64-bit launcher (batch file) mentioned below has been included.
  • GLZ-based methods now allow selection of distributions and link functions.
  • Known bug: With certain traits, MIM-contour "chatter" or instability is seen in wide marker intervals, and these contours take two or three times longer to compute.

1.28.10 Running QGene on a 64-bit computer

  • If your computer has a 64-bit architecture, the QGene.exe launcher won't work. Instead, use this .bat file with accompanying instructions. Thanks to LD for pointing out the problem. We will eventually compile a 64-bit QGene.exe launcher but at present don't have a suitable compiler and test machine.

7.22.09 Version 4.3.2 is released with these fixes or features:

  • Trait simulation was generating incorrect QTL genotypes, resulting in reversal of effect signs and slight displacement of peaks.
  • PMLE and MT-PMLE are now built exactly according to the specification in the paper.
  • Shrinkage IM and MT-Shrinkage IM have been modified to use MIM as the back end instead of CIM.
  • QGene allows QTL mapping with fewer progeny in the population (not that it's a good idea!). For a RIL design, you can use a population of 5 progeny. Thanks to MW for reporting the confusing error message.
  • Miscellaneous other rarely encountered bugs have been fixed.

6.16.09 Version 4.3.1 is released with these fixes or features:

  • Trait analysis that was crashing in some situations.
  • Heritability calculation for eQTL analysis (see eQTL analysis page).
  • The eQTL analysis should now be stable enough. It should be scalable to processors with many cores.
  • Miscellaneous other rarely encountered bugs have been fixed.
  • Some known bugs from 4.2.3 are still not fixed.

5.07.09 Version 4.3.0 is released with these new features:

  • QGene is faster due to more efficient multithreading routines.
  • The launcher has been improved and should be able to detect the Java JDK/JRE more smoothly.
  • A fast eQTL analysis is now in place. It may have some bugs, so please consider it a beta feature.
  • QGene eQTL analysis
  • Miscellaneous other rarely encountered bugs have been fixed.
  • Some known bugs from 4.2.3 are still not fixed.

News of previous releases.

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