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https://github.com/lczech/gappa
A toolkit for analyzing and visualizing phylogenetic (placement) data
https://github.com/lczech/gappa
c-plus-plus evolutionary-placement gappa genesis phylogenetic-data phylogenetic-placement phylogenetics placement
Last synced: 6 days ago
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A toolkit for analyzing and visualizing phylogenetic (placement) data
- Host: GitHub
- URL: https://github.com/lczech/gappa
- Owner: lczech
- License: gpl-3.0
- Created: 2017-10-20T09:27:09.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2024-06-28T13:35:45.000Z (4 months ago)
- Last Synced: 2024-10-15T17:57:59.584Z (22 days ago)
- Topics: c-plus-plus, evolutionary-placement, gappa, genesis, phylogenetic-data, phylogenetic-placement, phylogenetics, placement
- Language: C++
- Homepage:
- Size: 11.3 MB
- Stars: 56
- Watchers: 7
- Forks: 7
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
- Citation: CITATION.cff
Awesome Lists containing this project
README
[](https://anaconda.org/bioconda/gappa)
[](https://anaconda.org/bioconda/gappa)
[](https://github.com/lczech/gappa/releases)
[](https://doi.org/10.1093/bioinformatics/btaa070)
[](https://github.com/lczech/gappa/actions)
[](https://github.com/adrianzap/softwipe/wiki/Code-Quality-Benchmark)
[](https://anaconda.org/bioconda/gappa)
[](http://www.gnu.org/licenses/gpl.html)
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 are typically produced by tools such as [EPA-ng](https://github.com/Pbdas/epa-ng),
[RAxML-EPA](http://sco.h-its.org/exelixis/web/software/epa/index.html) or
[pplacer](http://matsen.fhcrc.org/pplacer/), and usually stored in
[jplace](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0031009) files.
See [**the Wiki pages**](https://github.com/lczech/gappa/wiki)
for the full list of all subcommands and their documentation.
We recommend our article ["Metagenomic Analysis Using Phylogenetic Placement — A Review of the First Decade"](https://doi.org/10.3389/fbinf.2022.871393) as an introduction to the topic of phylogenetic placement.
Setup
-------------------
There are two ways to get gappa:
1. Install it via [conda](https://anaconda.org/bioconda/gappa).
2. 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:
~~~.sh
git clone --recursive https://github.com/lczech/gappa.git
cd gappa
make
~~~
You can also use the green "Code" button above or
[click here](https://github.com/lczech/gappa/archive/master.zip) to download the source as a zip
archive. Unpack, and call `make` in the main directory to build everything.
Requirements:
* [Make](https://www.gnu.org/software/make/) and [CMake](https://cmake.org/) 3.1 or higher.
* A fairly up-to-date C++11 compiler, e.g.,
[clang++ 3.6](http://clang.llvm.org/) or [GCC 4.9](https://gcc.gnu.org/), 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
See [**the Wiki pages**](https://github.com/lczech/gappa/wiki)
for the full list of all subcommands and their documentation.
For **bug reports and feature requests** of gappa, please
[open an issue on GitHub](https://github.com/lczech/gappa/issues).
For **user support**, please see our
[Phylogenetic Placement Google Group](https://groups.google.com/forum/#!forum/phylogenetic-placement).
It is intended for discussions about phylogenetic placement,
and for user support for our software tools, such as [EPA-ng](https://github.com/Pbdas/epa-ng),
[gappa](https://github.com/lczech/gappa), and [genesis](https://github.com/lczech/genesis).
Citation
-------------------
**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
Each command also prints out the relevant references for that command. Then, the command [`gappa tools citation`](https://github.com/lczech/gappa/wiki/Subcommand:-citation) can be used to obtain details on those references. See also our Wiki page [Citation and References
](https://github.com/lczech/gappa/wiki/Citation-and-References) for a list of all references.
Lastly, we recommend reading our comprehensive review of the topic
> Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade.
> Lucas Czech, Alexandros Stamatakis, Micah Dunthorn, and Pierre Barbera.
> Frontiers in Bioinformatics, 2022. https://doi.org/10.3389/fbinf.2022.871393
to get an overview of phylogenetic placement and its methods.
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](https://github.com/lczech/genesis) library.
See there if you are interested in the implementation details.