Multivariate Analysis of Protein Polymorphism (MAPP)
MAPP is a method that aims to predict the deleteriousness of non-synonymous single nucleotide polymorphisms. MAPP expects an alignment of interspecific sequences that are putatively orthologous to the protein of interest. MAPP scores variant proteins on the basis of their “distance” from the alignment in physicochemical property space. MAPP was described in a 2005 article in Genome Research. A Java implementation can be downloaded here. There is a secret MAPP server (not so secret anymore) that can runs in your web browser. Feel free to try it out but please know that it is a neglected work in progress.
Modulated Modularity Clustering (MMC)
MMC is a graph-based clustering algorithm that seeks an optimal partitioning of hopefully not too many objects. The approach and its implementation were described in a 2009 PLoS Genetics article. A web server running MMC can be found here. Though MMC was motivated by gene expression data, it is by no means limited to it. Anyone interested in some theoretical work that sort of relates to MMC is welcome to click here.
Joint Genotyper for Inbred Lines (JGIL)
JGIL is the implementation of a probabilistic model designed to simultaneously genotype a panel of inbred lines or strains using next-generation sequence data. The model is introduced in a 2012 Genome Research article and was motivated by an application to the Drosophila Genetic Reference Panel (DGRP). Click here to dowload JGIL release 1.6. Release 1.6 supports merged bam files and corrects ar earlier bug that affected the quality of A/G "heterozygote" calls. An updated readme document is available here.