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The core S.A.G.E. source code
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S.A.G.E. (Statistical Analysis for Genetic Epidemiology) is a free software package containing programs for use in the genetic analysis of family, pedigree and individual data.

S.A.G.E. is a collection of freely available C++ programs that perform a wide variety of genetic analyses on both family data and data on unrelated individuals. The range of functionality includes tools for

• extracting summary statistics describing the data and evaluating general data quality,

• estimating allele frequencies and testing Hardy-Weinberg proportions,

• estimating heritability and familial correlations,

• inferring mixture models for genetic transmission and penetrance functions, including variable age of onset,

• estimating identity-by-descent (IBD) allele sharing probabilities between relative pairs,

• performing model-based linkage analysis,

• performing model-free linkage analysis,

• performing transmission/disequilibrium (TDT) analysis, and

• analyzing trait/allele associations in both family data and unrelated individuals.

S.A.G.E. runs on a variety of platforms: Linux, Windows, and Mac/OSX. The programs may be run either from a command line or from a cross-platform graphical user interface (GUI) that is included as part of the complete package. The software is extremely flexible with respect to the structure of input data files and, unless otherwise stated, the dependent traits may be discrete (including dichotomous data) or quantitative.

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