MapQTL and R/qtl are a powerful tools to do QTL mapping. They allow you to analyze quickly multiple traits, allowing high-throughput QTL mapping. However, if you perform QTL mapping on a lot of traits, it is hard to get an overview of the results. With MapQTL you can visualize the results but only one trait at a time, with R/qtl you need to have some basis of R programming.
MQ² aims at filling this need. Assuming one QTL per linkage group and using the LOD threshold set by the user, it extracts all the QTLs detected by MapQTL, R/qtl or any other QTL mapping tool, it finds the marker closest to the peak and finally calculates the number of QTLs found near each marker on the map. Note that this works for Interval mapping, MQM or RQM mapping but not for KW mapping.
This approach quickly allows you to find and visualize potential QTL hotspot in your dataset. This is particularly useful for QTL analyses on a large number of traits.
If you have any doubts/questions on how to use MQ², have a look at the documentation (pdf)!
Example input files:
The aim of this tool is to visualize Mapped QTLs.
So, it is Mapped QTLs to QTLs,
QTL * QTL = QTL²