SHOREmap v3.x (latest v3.6), is hold at http://bioinfo.mpipz.mpg.de/shoremap/ :
Whole genome resequencing of pools of recombinant mutant genomes allows directly linking phenotypic traits to causal mutations. Such an analysis, called mapping-by-sequencing, combines classical genetic mapping and next generation sequencing by relying on selection-induced patterns within genome-wide allele frequency in pooled genomes. SHOREmap is a computational tool implementing a method that enables simple and straightforward mapping-by-sequencing analysis.
SHOREmap was originally developed in the lab of Detlef Weigel and is continuously developed in the group of Korbinian Schneeberger. The latest version, SHOREmap v3.6, is developed in C/C++. Compared to the previous versions (version 2.0 or earlier), it has three new features. It accepts resequencing data that are generated in Variant Call Format (VCF), such as by SAMtools. It can make use of resequencing information of parental lines to define high-quality markers. It uses mean and coefficient of AF values to calculate stable mapping intervals. If you use SHOREmap v3.x, please cite the following publications.
For a detailed description on the usage of SHOREmap v3.x (example with v3.0),
Sun et al. (2015), "SHOREmap v3.0: fast and accurate identification of causal mutations from forward genetic screens". In: Alonso, J.M., and Stepanova, A.N. (Eds.), Plant Functional Genomics: Methods and Protocols (pp381-395), 2nd Edition, New York: Springer.
Schneeberger et al. (2009), "SHOREmap: simultaneous mapping and mutation identification by deep sequencing", Nature Methods.
For more information on SHOREmap,
B. Hartwig et al.(2012), "Fast isogenic mapping-by-sequencing of EMS-induced mutant bulks", Plant Physiology. Galvão et al. (2012), "Synteny-based Mapping-by-Sequencing enabled by Targeted Enrichment", Plant Journal.
For more general information on mapping-by-sequencing,
Schneeberger K (2014). Using next-generation sequencing to isolate mutant genes from forward genetic screens. Nature Rev. Genet.