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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.
There are several dependencies required to run SuperCRUNCH, including Python packages (BioPython and numpy), as well as external tools (NCBI-BLAST+, CD-HIT-EST, MAFFT, Muscle, Clustal-O, MACSE, and trimAl).
Installation of these requirements is fast and easy using conda, but they can also be installed manually. Instructions for both can be found on the Installation Instructions wiki.
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 several available 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.
A new set of tutorials is available as part of a study testing alignment and trimming combinations (Portik & Wiens, 2021 - Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses?). The complete set of data and instructions are available at https://osf.io/qa9r8/.
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 (daniel.portik@gmail.com)