This page includes links to software and web services. Updates will be posted here.

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 and associated files can be downloaded here. 

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. Feel free to try it out on your favorite data type!

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 melanogasterGenetic Reference Panel (DGRP). Click here to download 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.

Please note that JGIL is not restricted to Drosophila sequence data. Moreover, it can be applied to haploids by setting the number of generations to be large.

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