QTX

software for complex trait analysis

by Jane M. Meer, Robert H. Cudmore, Jr., and Kenneth F. Manly

Table of Contents Current Version is b20 Recent History Library Files Sample Data Files Other Mapping Software

News QTXb20 !! 04/21/04 - Release QTXb20 with versions for Mac OS X/9, and Windows NT/2K/XP 08/15/04 - Relocation of the Map Manager lab means that we will no longer be able to supply software and manuals by mail. If you have bad news, we have a bug report form

Just the Downloads QTX for Windows (also download libraries; see below) Libraries for Windows (updated for b18; dlls before b18 will not work with this version) QTX for Mac (needs Classic/OS9 to self-extract) QTX for Mac (needs Stuffit Expander) Hypertext tutorial PDF manual PDF tutorial

Development and distribution of QTX has been supported by a grant from the Rockefeller Foundation and by grant HG01656 from the National Human Genome Research Institute, National Institutes of Health. Citation for QTX: Manly, KF, Cudmore, Jr, RH, Meer, JM (2001) Map Manager QTX, cross-platform software for genetic mapping. Mammalian Genome 12: 930-932.

Library (.dll) files The Windows version requires library files if you have not previously downloaded them. The libraries should be put into the same folder as the QTX program, or they should be put into the folder with other dll files (C:/windows or C:/Winnt/system32, for example). These libraries are available as a self-extracting zip file. Some people report that they also need the msvcrt.dll or msvcrt40.dll libraries, also available as a self-extracting zip file. For the b18 version, some have reported needing msvci70.dll or msvcr70.dll.

---

QTX combines the cross-platform design and convenient quantitative locus mapping.

• It allows detection and localization of quantitative trait loci by fast regression-based single locus association, simple interval mapping, composite interval mapping, and search for interacting QTLs.
• It calculates empirical significance values by permutation tests and by the quick method of Piepho.
• It allows a choice of Haldane, Kosambi, and Morgan mapping functions.
• It supports advanced backcross, advanced intercross, and recombinant inbred intercross (RIX) designs.
• It creates cross-platform data files which are compatible with both MS Windows and Mac OS versions of QTX.
  QTX and Map Manager QT (version b26 or later) will each read files created by the other.
  The Mac OS version of QTX will read (but not write) files created by Map Manager Classic.

Abbreviated version history.

Version 20 adds a report for the bootstrap analysis and fixes several bugs. More details in the version history page.

Version 19 introduces a single Mac version that runs on OS 9/Classic/OS X.

Version 18 introduces a version for Mac OS X and several bug fixes.

Version 17 introduces improved support for datasets with over 1000 progeny and fixes several bugs.

Version 16 introduces bootstrap analysis to estimate confidence regions for QTLs.

Version 15 fixes three bugs introduced with the new features of 14. These are (1) trait variances are ignored if you try to use them for weighted regression (2) "invalid rectangle" error messages occur during an interaction permutation test and (3) interaction report fails to be created or crashes on display.

Sample Data

A set of sample data files is available for Mac or Win. These include a QTX file with a simulated intercross involving four traits and text files to demonstrate importing marker data and trait data into Map Manager. There is also a set of tutorial exercises developed for a genetics lab which use the sample data files.