QTL IciMapping is freely-available public software capable of building high-density genetic maps and mapping quantitative trait loci (QTLs). Compared with previous versions, the latest version has five new features: dominant/recessive markers are considered in recombination frequency estimation, map construction and QTL mapping; a new functionality called IMP can be used to build an integrated map from multiple genetic linkage maps sharing common markers; a new tool called 2pointREC can be used to estimate the pair-wise recombination frequency in biparental populations; many more markers can be handled by this software— for example, it can perform map construction and QTL mapping of more than 5000 markers; and linkage map figures are improved. The software is project-based; kernel modules for building linkage maps were written using C#, those for QTL mapping were written using Fortran 90/95, and the interface was written using C#. QTL IciMapping runs on 32 and 64-bit computers with Windows XP/Vista/7 and .NET Framework 2.0(x86)/3.0/3.5. Research and development of the software was supported mainly by the CGIAR Generation Challenge Program, National 863 Program, 973 Program, and the Natural Science Foundation of China. The latest version is freely available (here).
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