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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.

General usage

Most of the options are listed in the same order in which they are applied. That way, the list of options can be read top to bottom, to see what is happening to the flow of data at each point. We here walk through the options in that order as well.

• Build instructions
• Input formats
• Windowing

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
cathedral-plot	Create a cathedral plot, using the pre-computated cathedral data.
citation	Print references to be cited when using grenedalf.
diversity	Compute pool-sequencing corrected diversity measures Theta Pi, Theta Watterson, and Tajima's D.
frequency	Create a table with per-sample and/or total base counts and/or frequencies at positions in the genome.
fst	Compute pool-sequencing corrected measures of FST.
fst-cathedral	Compute the data for an FST cathedral plot.
license	Show the license of grenedalf.
simulate	Create a file with simulated random frequency data.
sync	Create a sync file that lists per-sample base counts at each position in the genome.
version	Extended version information about grenedalf.