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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 that function as stand-alone command-line scripts. These modules are compatible with Python 2 and Python 3. 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 including usage for all modules, proposed workflows, and common issues.
New tutorials corresponding to the updated version of SuperCRUNCH (v1.2) are being built and will be available soon. Please check back!
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])