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grenedalf is a collection of commands for working with population genetic data.

Many commands in grenedalf are re-implementations of commands of the PoPoolation and PoPoolation2 tools. However, being written in C++, grenedalf is much faster and needs less memory for most of the tasks.

Command Line Interface

grenedalf is used via its command line interface, with commands for each task. The commands have the general structure:

grenedalf <command> [options]

Commands:

Command	Description
afs-heatmap	Create a per-window heatmap of the allele frequency spectrum along the genome.
citation	Print references to be cited when using grenedalf.
diversity	Compute the pool-sequencing corrected diversity measures Theta Pi, Theta Watterson, and Tajima's D, following the PoPoolation approach, for each sample, in windows along the genome.
frequency	Create a table with per-sample and/or total base counts and/or frequencies at positions in the genome.
fst	Compute FST in windows or at individual positions along the genome.
license	Show the license of grenedalf.
simulate	Create a file with simulated random frequency data.
sync-file	Create a PoPoolation2 sync file that lists per-sample base counts at each position in the genome.
version	Extended version information about grenedalf.