Genesis Applications for Phylogenetic Placement Analysis
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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. 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.


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

git clone --recursive
cd gappa

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


After building, the executable is stored in the bin directory, and used as follows.

Command Line Interface

gappa is used via its command line interface, with subcommands for each task. The subcommands have the general structure:

gappa <module> <subcommand> <options>

For a list of all subcommands and their documentation, see the Wiki pages.

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.