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Software
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ConvertCufflinksToExcel

This program converts several Cufflinks output files into easily readable Microsoft Excel tables using Apache's POI library. Only the "cuffdiff" output format currently is supported, but future versions may include other output formats.

 

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FINDHAP

The findhap.f90 program finds haplotypes and imputes genotypes using multiple chip sets and sequence data.

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FINDMAP

The findmap.f90 program aligns sequence reads to reference map, calls previous variants, and identifies new variants.

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GENOSIM

The genosim package simulates genotypes, breeding values, and phenotypes; simulates DNA sequence read depth (numbers of A and B alleles); and resolves SNP conflicts between parent and offspring genotypes.

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