mummer4.github.io/index.html at master · mummer4/mummer4.github.io · GitHub

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    <title>MUMmer</title>
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            <h1>Description</h1>
<p>MUMmer is a system for rapidly aligning large DNA sequences to one another. It can align:
    <ul>
        <li>whole genomes to other genomes</li>
        <li>large genome assemblies to one another</li>
        <li>partial (draft) genomes sequences to one another</li>
        <li>or (with release 4) a set of reads to a genome.</li>
            </ul>
    MUMmer is very fast and easy to run. The current version, release 4.x, can find all 20-bp maximal exact matches between two bacterial genomes in just a few seconds on a typical desktop or laptop computer. MUMmer handles the 100s or 1000s of contigs from a draft genome with ease, and will align them to another set of contigs using the nucmer utility included with the system. The promer utility takes this a step further by generating alignments based upon the six-frame translations of both input sequences. Most of the improvements in release 4.x are to nucmer and MUMmer. Promer is unchanged from release 3.0. See the nucmer and promer readme files in the "docs/" subdirectory for more details. <br/>
    MUMmer is free and open source, so all we ask is that you cite our most recent paper in any publications that use it. Here are the relevant publications:
            <h4>Version 4.0+</h4>
            <p>MUMmer4 and nucmer4 are described in "<a href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005944">MUMmer4: A fast and versatile genome alignment system</a>" G. Marçais , A.L. Delcher, A.M. Phillippy, R. Coston, S.L. Salzberg, A. Zimin, <em>PLoS computational biology</em> (2018), 14(1): e1005944.</p>
            <h4>Version 3.0</h4>
            <p>Open source MUMmer 3.0 is described in "<a href="publications/MUMmer3.pdf">Versatile and open software for comparing large genomes</a>." S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway, C. Antonescu, and S.L. Salzberg, <em>Genome Biology</em> (2004), 5:R12.</p>
            <h4>Version 2.1</h4>
            <p>MUMmer 2.1, NUCmer, and PROmer are described in "<a href="publications/MUMmer2.pdf">Fast Algorithms for Large-scale Genome Alignment and Comparision</a>." A.L. Delcher, A. Phillippy, J. Carlton, and S.L. Salzberg, <em>Nucleic Acids Research</em> (2002), Vol. 30, No. 11 2478-2483.</p>
            <h4>Version 1.0</h4>
            <p>MUMmer 1.0 is described in "<a href="publications/MUMmer.pdf">Alignment of Whole Genomes</a>." A.L. Delcher, S. Kasif, R.D. Fleischmann, J. Peterson, O. White, and S.L. Salzberg, <em>Nucleic Acids Research</em>, 27:11 (1999), 2369-2376.</p>
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                <h2>About Us</h2>
                    <p>MUMmer4 and nucmer4 were developed by Guillaume Marcais (CMU/UMD) and Aleksey Zimin (UMD/JHU), building on MUMmer3 and nucmer3. The development and support team also includes Adam Phillippy (NIH), Daniela Puiu (JHU), and Steven Salzberg (JHU).</p>
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            <section class="Column">
                <h2>Useful Links</h2>
                <ul>
                    <li>
                        <a class="footSub" href="https://github.com/mummer4/mummer">MUMmer4 at Github</a>
                    </li>
                    <li>
                        <a class="footSub" href="http://mummer.sourceforge.net/">MUMmer3 at SourceForge</a>
                    </li>
                </ul>
            </section>
            <section class="Column">
                <h2>Acknowledgements</h2>
                    <p>The development of early versions of MUMmer, particularly MUMmer3, was supported in part by NSF under grants IIS-9902923 (S. Salzberg) and IIS-9820497 (A. Delcher), and by NIH under grants R01-LM06845 to Steven Salzberg. MUMmer 1.0 and 2.0 were developed by Art Delcher, Steven Salzberg and colleagues (see the papers for other authors). MUMmer3.0 was a joint development effort by Stefan Kurtz of the University of Hamburg, Adam Phillippy, Art Delcher and Steven Salzberg, who were all at TIGR until 2005. <br>
                    MUMmer4 is currently supported in part by NIH under grant R01-GM083873 to Steven Salzberg.</p>
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