The QTL café is a JAVA based package which provides a user friendly way to perform QTL analyses. It is designed for those who want rapid analysis and interpretations of their data without requiring extensive statistical and computing skills. Moreover, the software works and looks the same on any platform, PC, Macintosh or UNIX

The QTL café has the following features at the push of a button:

		Easy and flexible data loading.
		Simple menu driven analyses.
		Statistical and graphical output.
		Easy export of data or graphical images.

1. Types of population:

The software to date is designed to analyse most populations derived from pure line crosses, ie: F₂s, backrosses, recombinant inbred lines and doubled haploid lines. It will shortly be extended to multiline and pedigree populations.

2. Data formats:

The software requires 3 data files

		A map file indicating the name and location of your markers.
		A genotype file containing the genotypes of your population. This file can be in MAPMAKER, JOINMAP or any defined alternative format.
		A trait file containing the names and scores of your traits.

3. Analyses:

The software currently allows 3 types of QTL analysis

		Single marker ANOVA.
		Marker regression (Kearsey and Hyne, Theor. Appl. Genet., 89, 698-702, 1994).
		Interval mapping by regression (Haley and Knott, Heredity 69, 315-324, 1992).

It also allows you to:

		look at the basic statistics of your trait distribution.
		look at the distribution of the trait data in histogram form.
		transform or modify your trait data.
		select or exclude markers and/or lines.
		check on segregation distortion.
		check on missing marker data.
		draw maps of markers and QTL.
		compare observed and expected marker means graphically.
		include multiple QTL per chromosome.
		click and drag facilities to check fit with candidate loci.
		choose the particular chromosome and trait to analyse.

THE QTL APPLET