27 research outputs found

    TMC.tar

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    Here we provide executable code for TMC algorithm, instructions for usage, input/output data formats and few example

    wQMC_testPack

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    A test package for wQMC for generating the data that is given in the pape

    Performance of the identification under weaker PM signal (variance) .

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    <p><i>p</i>-value of the <i>χ</i><sup>2</sup> is plotted versus the amount of noise. Each curve represent a different number of sites from {10, 20 30} (a) 50 individuals (b) 100 individuals.</p

    Human data.

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    <p>(<b>a</b>) <i>Rate Acceleration/Deceleration under PM vs MC</i>: Curve indicates the MC/PM rates respectively at each site in the study. As can be seen, rates generally maintain their original sign under both MC and PM however some sites accelerate and others decelerate. (<b>b</b>) <i>Age Acceleration/Deceleration under PM vs MC</i>: Ages were sorted in ascending sequence. For every time, the ratio between the PM inferred time to real chronological time is plotted.</p

    The <i>mn</i> Ă— 2<i>n</i> matrix <i>X</i> that is used in our closed form solution to the MC case.

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    <p>Every row corresponds to a component in the RSS polynomial and the corresponding entries (<i>i</i>th and <i>i</i> + <i>n</i>th) in that row are set to <i>t</i><sub><i>j</i></sub> and 1 respectively.</p

    Molecular clock vs Universal PaceMaker.

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    <p>(<b>a</b>) Under the Molecular Clock (MC) model, methylation rates of sites differ among each other but are constant in time. (<b>b</b>) By contrast, under the Universal PaceMaker (UPM) model (right), rates may vary during with time but the pairwise ratio between sites rates remains constant.</p

    Comparison of the Molecular Clock and Universal Pacemaker models of genome evolution.

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    <p>Comparison of the Molecular Clock and Universal Pacemaker models of genome evolution.</p
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