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Lucas Czech edited this page Jun 6, 2024
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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.
grenedalf is used via its command line interface, with commands for each task. The commands have the general structure:
grenedalf <command> [options]
Use grenedalf --help to get an overview of all commands, and use grenedalf <command> --help for the list of options of each command. The pages below also list these options, along with additional information on each command.
| 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. |