Features
gappa is a collection of commands for working with phylogenetic data. Its main focus are evolutionary placements of short environmental sequences on a reference phylogenetic tree. Such data is typically produced by tools like EPA-ng, RAxML-EPA or pplacer and usually stored in jplace files.
Many commands in gappa are implementations of our novel methods as described in
Methods for Inference of Automatic Reference Phylogenies and Multilevel Phylogenetic Placement.
Lucas Czech, Pierre Barbera, and Alexandros Stamatakis.
Bioinformatics, 2018. https://doi.org/10.1093/bioinformatics/bty767
and
Scalable Methods for Analyzing and Visualizing Phylogenetic Placement of Metagenomic Samples.
Lucas Czech and Alexandros Stamatakis.
PLOS One, 2019. https://doi.org/10.1371/journal.pone.0217050
At the same time, it offers some commands that are also implemented in the excellent guppy tool. However, being written in C++, our gappa is much faster and needs less memory for most of the tasks.
Setup
There are two ways to get gappa:
- Install it via conda.
- Build it from source.
While conda will only give you proper releases, building from source will give you the latest (development) version. For that, simply get it, and build it:
git clone --recursive https://github.com/lczech/gappa.git
cd gappa
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.
Usage and Documentation
gappa is used via its command line interface, with subcommands for each task. The commands have the general structure:
gappa <module> <subcommand> <options>
See the Wiki pages for the full list of all subcommands and their documentation.
For bug reports and feature requests of gappa, please open an issue on GitHub.
For user support, please see our Phylogenetic Placement Google Group. It is intended for discussions about phylogenetic placement, and for user support for our software tools, such as EPA-ng, gappa, and genesis.
Citation
When using gappa commands, they will output the necessary citations for the command.
To generally cite gappa, please use
Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data.
Lucas Czech, Pierre Barbera, and Alexandros Stamatakis.
Bioinformatics, 2020. https://doi.org/10.1093/bioinformatics/btaa070
Furthermore, the command gappa tools citation can be used to obtain a full list of relevant references.
Behind the scenes
gappa is short for Genesis Applications for Phylogenetic Placement Analysis. This is because most of the work of gappa is actually performed by our genesis library. See there if you are interested in the implementation details.