grenedalf is a collection of commands for working with population genetic data, in particular from pool sequencing. Its main focus are statistical analyses such as Tajima's D and Fst. The statistics follow the approaches of PoPoolation and PoPoolation2, as well as poolfstat and npstat. However, compared to those, grenedalf is significantly more scalable, more user friendly, and offers more settings and input file formats.
Feedback on functionality, interface, and features is highly appreciated!
We recommend to first try the pre-compiled binaries of the latest Release, by downloading the binary for your system from the "Assets" list below the release. If that does not work, grenedalf can be build from source as described here.
grenedalf is used via its command line interface, with commands for each task. The commands have the general structure:
grenedalf <command> <options>
See the Wiki pages for the list of all commands and their documentation.
Please find the preprint here:
grenedalf: population genetic statistics for the next generation of pool sequencing.
Lucas Czech, Jeffrey P. Spence, Moisés Expósito-Alonso.
arXiv, 2023. arXiv:2306.11622
Each command also prints out the relevant references for that command. Then, the command grenedalf citation can be used to obtain details on those references.