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, following the approaches of PoPoolation and PoPoolation2.
Remark: grenedalf is quite young and in activate development. The interface will change frequently in the near future. Until we publish a release version, everything is considered to be in beta status. Feedback on functionality, interface, and features is highly appreciated!
To run grenedalf on your machine, simply get it, and build it:
git clone --recursive https://github.com/lczech/grenedalf.git
cd grenedalf
makeYou can also use the green "Code" button above or
click here to download the source as a zip
archive. Unpack, and call make in the main directory to build everything.
Requirements:
- Make and CMake 2.8.7 or higher.
- A fairly up-to-date C++11 compiler, e.g., clang++ 3.6 or GCC 4.9, or higher.
After building, the executable is stored in the bin directory, and used as follows.
grenedalf is used via its command line interface, with commands for each task. The commands have the general structure:
grenedalf <command> <options>
Use the --help flag of grenedalf or of each command for usage information.
See the Wiki pages
for the full list of all subcommands and their documentation.