Home

Menu

Loading wiki pages...

View
Wiki Version:
<p><img alt="Logo" src="https://files.osf.io/v1/resources/bpt94/providers/osfstorage/5c56175de16f55001887b55a?mode=render"></p> <hr> <p><strong>SuperCRUNCH</strong> is a program used to create, filter and manipulate large phylogenetic data sets based on downloaded and/or local sequence data. <strong>SuperCRUNCH</strong> is described in detail in the following pre-print:</p> <p>Portik, D.M., and J.J. Wiens. (2019) SuperCRUNCH: A toolkit for creating and manipulating supermatrices and other large phylogenetic datasets. BioRxiv, <a href="https://doi.org/10.1101/538728" rel="nofollow">https://doi.org/10.1101/538728</a>.</p> <p>This page contains all the information and files required to reproduce the analyses used to introduce SuperCRUNCH:</p> <p><strong>SuperCRUNCH - Iguania (NCBI starting sequences):</strong> + Building a supermatrix for Iguania using SuperCRUNCH and sequences downloaded directly from NCBI.</p> <p><strong>SuperCRUNCH - Iguania (PyPHLAWD starting sequences):</strong> + Building a supermatrix for Iguania using SuperCRUNCH and sequences downloaded through PyPHLAWD.</p> <p><strong>PyPHLAWD - Iguania:</strong> + Building a supermatrix for Iguania using PyPHLAWD.</p> <p><strong>SuperCRUNCH - Dipsacales (PyPHLAWD starting sequences):</strong> + Building a supermatrix for Dipsacales using SuperCRUNCH and sequences downloaded through PyPHLAWD.</p> <p><strong>PyPHLAWD - Dipsacales:</strong> + Building a supermatrix for Dipsacales using PyPHLAWD.</p> <p><strong>SuperCRUNCH - UCE data:</strong> + Building a supermatrix of UCE loci using SuperCRUNCH for the frog genus <em>Kaloula</em>.</p> <p><strong>SuperCRUNCH - Population-level data (<em>Uma</em>):</strong> + SuperCRUNCH analysis to retrieve population level data for the lizard genus <em>Uma</em>.</p> <p><strong>SuperCRUNCH - Population-level data (<em>Callisaurus</em>):</strong> + SuperCRUNCH analysis to retrieve population-level data for the lizard genus <em>Callisaurus</em>.</p> <p>For each analysis listed above, there is a corresponding page that contains all input files, output files, and a comprehensive wiki tutorial. This data and information will allow each analysis to be replicated.</p>
OSF does not support the use of Internet Explorer. For optimal performance, please switch to another browser.
Accept
This website relies on cookies to help provide a better user experience. By clicking Accept or continuing to use the site, you agree. For more information, see our Privacy Policy and information on cookie use.
Accept
×

Start managing your projects on the OSF today.

Free and easy to use, the Open Science Framework supports the entire research lifecycle: planning, execution, reporting, archiving, and discovery.