Software:


Multiplexed Shotgun Genotyping (MSG).

A pipeline of scripts to assign ancestry to genomic segments using next-gen sequence data.  This method can identify recombination breakpoints in a large number of individuals simultaneously at a resolution sufficient for most mapping purposes, such as quantitative trait locus (QTL) mapping and mapping of induced mutations.


Andolfatto P, Davison D, Erezyilmaz D, Hu TT, Mast J, Sunayama-Morita T, Stern DL. 2011. Multiplexed Shotgun Genotyping for Rapid and Efficient Genetic Mapping.  Genome Research, 21: 610-7. [link].


simMSG.

A computational experimental design tool for MSG experiments. MSG can be a powerful tool for low cost genotyping of artificial and natural hybrids but accuracy depends on the density of ancestry informative sites between the parental genomes, the number of generations of recombination, polymorphism levels, as well as features of the experimental design such as coverage. simMSG allows users to predict MSG's accuracy in their system and determine the amount any type of sequencing effort required.


Schumer M, Cui R, Rosenthal GG, Andolfatto P. 2015. simMSG: an experimental design tool for high-throughput genotyping of hybrids. Mol Ecol Resour. 16:183-92. [link]



Older software:


MK-Pvalues. R-script to assess the type-I error and true P-value of the McDonald-Kreitman test (Andolfatto 2008, Genetics). MK_pvalues.zip.


Polymorphorama. (Andolfatto 2007, Genome Res; Haddrill et al, 2008, MBE) is an evolving library of scripts for population genetic data analysis of fasta aligned coding and non-coding sequences [in progress]. Polymorphorama.zip.


Multilocus tests of neutrality. Download programs that can be used to summarize real and simulated data and perform multilocus tests of neutrality with recombination as implemented in Haddrill et al. Genome Research (2005). To generate simulated genealogies as input for this program, please use Dick Hudson's program "ms". Real data must be in an "ms-like" format and polymorphisms must be properly polarised with respect to the outgroup sequence. The outgroup sequence must be the last sequence in each real or simulated dataset.


Sliding Window Strobeck's Test (SWST) of Andolfatto et al. (1999) - Download unix source code files. A test of the neutral equilibrium haplotype structure based on Strobeck (1987) that corrects both for multiple tests and for an arbitrarily chosen window size.


Speciation Time Estimator (STE) of Bachtrog et al. (2006 Evolution) and Putnam et al. (2007 Evolution) - Download.