This is an archived static version of the original discussion site.

New software for supermtatrices of many genes/species


SuperCRUNCH is a python toolkit for extracting, filtering, and manipulating nucleotide data. SuperCRUNCH uses sequence data downloaded directly from NCBI as a starting point, rather than retrieving sequences through an intermediate step (GenBank database releases and/or NCBI Taxonomy). Sequence sets are created based on designated lists of taxa and loci, offering fine-control for targeted searches. SuperCRUNCH includes refined methods for orthology detection and sequence selection. By offering the option to select representative sequences for taxa or retain all filtered sequences, SuperCRUNCH can be used to generate interspecific supermatrix datasets (one sequence per taxon per locus) or population-level datasets (multiple sequences per taxon per locus). It can also be used to assemble phylogenomic datasets with thousands of loci. SuperCRUNCH is modular in design, and was intended to be transparent, objective and repeatable.

A full overview of SuperCRUNCH is described in the following pre-print article:

  • Portik, D.M., and J.J. Wiens. (2019) SuperCRUNCH: A toolkit for creating and manipulating supermatrices and other large phylogenetic datasets. BioRxiv,