The MiModD suite of tools, developed in the Baumeister lab at the Institute for Biology 3 here in Freiburg, is now available on the server. MiModD is for geneticists who have isolated phenotypic mutants of their favourite organism, e.g., through forward genetic screens, and who now wish to map the underlying mutations and eventually identify them molecularly.
Provided you have followed a mutant phenotype through a cross between the mutant line and a suitable mapping strain and have sequenced recombinant offspring genomes, you can use the MiModD tools to identify marker SNPs (inherited from either parent) and perform a linkage analysis between these markers and the observed phenotype. You can then continue with MiModD to identify and annotate candidate mutations that fall into the linked genomic region.
MiModD can derive linkage patterns from a variety of different crossing schemes and has been used successfully for species as diverse as the ciliate Tetrahymena thermophila, the roundworm C. elegans, and zebrafish.
A Galaxy-based tutorial for the tools is available here and there is also a shared workflow to reproduce the analysis from the tutorial. Additional example analyses can be found in the MiModD documentation.