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README.md

gappa

Build Status License Language

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

To run gappa on your machine, simply get it, and build it:

git clone --recursive https://github.com/lczech/gappa.git
cd gappa
make

You can also use the green "Clone and download" button to get the source. Still, call make in the main directory to build everything.

Requirements:

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.

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.

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