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Welcome to the SuperCRUNCH wiki! These pages are intended to help you get SuperCRUNCH up and running, and also help guide your analyses.
SuperCRUNCH SuperCRUNCH consists of a set of modules written in python (2.7) that function as stand-alone command-line scripts. These modules are available in the supercrunch-scripts folder. They can be downloaded and executed independently without the need to install SuperCRUNCH as a PYTHON package or library, making them easy to use and edit. The scripts function independently, and do not require being contained or used from the same directory. There are several external dependencies that should be installed prior to use of SuperCRUNCH, including:
Helpful installation instructions for these dependencies can be found on the wiki installation page.
An overview of the components of SuperCRUNCH can be found on the Analysis Overview wiki. This page outlines all major topics and navigates to detailed instructions for all major topics, including usage for all modules, proposed workflows, and common issues.
Several example analyses are available on the SuperCRUNCH project page on the Open Science Framework, including all input files, output files, and complete wiki tutorials. These analyses include:
- Iguania Supermatrix: SuperCRUNCH analysis of Iguania using sequence data downloaded directly from NCBI. Direct link.
- UCE Supermatrix: SuperCRUNCH analysis of UCE loci available for the frog genus Kaloula, using sequence data downloaded directly from NCBI. Direct link.
- Population Dataset (Uma): SuperCRUNCH analysis to retrieve population-level data for the lizard genus Uma, using sequence data downloaded directly from NCBI. Direct link.
- Population Dataset (Callisaurus): SuperCRUNCH analysis to retrieve population-level data for the lizard genus Callisaurus, using sequence data. Direct link.
Several example files are also provided in the data folder. These include locus search terms files and reference sequence sets.
SuperCRUNCH is currently described in a pre-print available on BioRxiv:
- 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.
SuperCRUNCH is also in peer-review, and we hope to have a formal publication soon.
If you use SuperCRUNCH for your research, please cite the above BioRxiv publication (for now).
GNU Lesser General Public License v3.0
SuperCRUNCH is written and maintained by Daniel Portik ([email protected])