libsequence: a C++ class library for evolutionary genetic analysis

By Kevin R. Thornton. Bioinform., 2003

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Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars (2013, methodology): “Basic summary statistics for each SNP (MAF, average pairwise diversity π) were calculated in the R package genetics and the libsequence C++ library (52).”
Identification of a functional transposon insertion in the maize domestication gene tb1 (2011, methodology): “Diversity analyses were performed using the “compute” program of the analysis package of libsequenc”
Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. (2009, methodology): “Polymorphism information was extracted from sequence alignments using the Libsequence evolutionary genetics software package (Thornton 2003).”