SuperCRUNCH

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Affiliated institutions: University of Arizona

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Description: Welcome to the OSF project page for SuperCRUNCH.

License: GNU General Public License (GPL) 3.0

Wiki

SuperCRUNCH is a program used to create, filter and manipulate large phylogenetic data sets based on downloaded and/or local sequence data. SuperCRUNCH is described in detail in the following pre-print: Portik, D.M., and J.J. Wiens. (2019) SuperCRUNCH: A toolkit for creating and manipulating supermatrices and other large phylogenetic datasets. BioRxiv, https://doi.org/10.1101/538728. This page c...

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Components

  • SuperCRUNCH: Iguania (NCBI starting sequences)

    SuperCRUNCH analysis of the Iguania starting sequence set downloaded directly from NCBI.

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  • SuperCRUNCH: Iguania (PyPHLAWD starting sequences)

    SuperCRUNCH analysis of the Iguania starting sequence set generated from PyPHLAWD.

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  • PyPHLAWD: Iguania

    PyPHLAWD analysis of Iguania.

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  • SuperCRUNCH: Dipsacales (PyPHLAWD starting sequences)

    SuperCRUNCH analysis of the Dipsacales starting sequence set generated from PyPHLAWD.

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  • PyPHLAWD: Dipsacales

    PyPHLAWD analysis of Dipsacales.

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  • SuperCRUNCH: UCE data

    SuperCRUNCH analysis of UCE loci from the frog genus Kaloula.

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  • SuperCRUNCH: Population-level data (Uma)

    SuperCRUNCH analysis to retrieve population level data for the lizard genus Uma.

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  • SuperCRUNCH: Population-level data (Callisaurus)

    SuperCRUNCH analysis to retrieve population-level data for the lizard genus Callisaurus.

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  • Supermatrix Files from All Analyses

    The final concatenated alignments from the analyses of Iguania and Dipsacales using SuperCRUNCH and PyPHLAWD.

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  • Supermatrix Phylogenies

    Bootstrapped phylogenies resulting from RAxML analyses on three Iguania and two Dipsacales supermatrices.

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