https://sourceforge.net/p/ntx/wiki/Home/Recent changes to HomeenTue, 12 Mar 2013 18:13:43 -0000https://sourceforge.net/p/ntx/wiki/Home/<div class="markdown_content"><p>This repository comprises the code for some utilities to manipulate the so-called "site frequency spectrum". A site frequency spectrum is a standard way to describe patterns of genomic variation among a sample of individuals. Its form can be influenced by selection, demography and other factors and this is exploited to infer aspects of evolutionary history out of present DNA sequences. Of particular interest are regions within a genome which experienced a form of selection in the recent past of the specie. Several tests on "neutrality" have been developed for this end. Those are implemented in the main tool "ntx", together with an extension to allow for the inclusion of demographic effects. </p> <h2 id="ntx">ntx</h2> <p>reads a frequency spectrum from console and calculates several test statistics. Arbitrary first and second moments of the frequency spectrum under the null hypothesis can be specified (corresponding to different demographies).</p> <h2 id="ntmom">ntmom</h2> <p>calculates the (exact) first and second moments under the assumption of a population of constant size. The formulas were derived by Fu 1995.</p> <h2 id="fs2mom">fs2mom</h2> <p>calculates the first and second moments out of a series of measured (or simulated) frequency spectra</p> <h2 id="ms2fs">ms2fs</h2> <p>computes the site frequency spectrum from the output of 'ms', a broadly used simulation program for genetic sequences.</p></div>A. KlassmannTue, 12 Mar 2013 18:13:43 -0000https://sourceforge.net0fef768b629bda1cd0df1213738da7a2d082f80ahttps://sourceforge.net/p/ntx/wiki/Home/Welcome to your wiki! This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage]. The wiki uses [Markdown](/p/ntx/wiki/markdown_syntax/) syntax. [[project_admins]] [[download_button]] A. KlassmannWed, 07 Nov 2012 13:18:15 -0000https://sourceforge.net81fa197e4dc5a13cee990436ce66a1dcd1984019