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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 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.
There are currently nine tutorials, which cover the full range of analyses run in the SuperCRUNCH publication. These tutorials can be found on the OSF SuperCRUNCH project page. Each tutorial includes all data and instructions necessary to replicate the analysis. An overview of the available tutorials can be found on the Tutorials wiki.
SuperCRUNCH was published as:
- Portik, D.M., and J.J. Wiens. (2020) SuperCRUNCH: A bioinformatics toolkit for creating and manipulating supermatrices and other large phylogenetic datasets. Methods in Ecology and Evolution, 11: 763-772. https://doi.org/10.1111/2041-210X.13392
GNU Lesser General Public License v3.0
SuperCRUNCH is written and maintained by Daniel Portik ([email protected])