{"id":17119741,"url":"https://github.com/lczech/gappa","last_synced_at":"2025-04-10T02:29:36.336Z","repository":{"id":51163735,"uuid":"107658853","full_name":"lczech/gappa","owner":"lczech","description":"A toolkit for analyzing and visualizing phylogenetic placement 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Genesis Applications for Phylogenetic Placement Analysis --\u003e\n\n[![Conda install](https://img.shields.io/conda/vn/bioconda/gappa)](https://anaconda.org/bioconda/gappa)\n[![Downloads](https://img.shields.io/conda/dn/bioconda/gappa)](https://anaconda.org/bioconda/gappa)\n[![Release](https://img.shields.io/github/v/release/lczech/gappa.svg)](https://github.com/lczech/gappa/releases)\n[![CI](https://github.com/lczech/gappa/actions/workflows/ci.yaml/badge.svg)](https://github.com/lczech/gappa/actions/workflows/ci.yaml)\n\u003cbr /\u003e\n[![License](https://img.shields.io/badge/license-GPLv3-blue.svg)](http://www.gnu.org/licenses/gpl.html)\n[![Softwipe Score](https://img.shields.io/badge/softwipe-9.0/10.0-blue)](https://github.com/adrianzap/softwipe/wiki/Code-Quality-Benchmark)\n[![DOI](https://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbtaa070-blue)](https://doi.org/10.1093/bioinformatics/btaa070)\n\u003c!-- [![Platforms](https://img.shields.io/conda/pn/bioconda/gappa)](https://anaconda.org/bioconda/gappa) --\u003e\n\u003c!-- ![Language](https://img.shields.io/badge/language-C%2B%2B11-lightgrey.svg) --\u003e\n\u003c!-- [![CI](https://github.com/lczech/gappa/workflows/CI/badge.svg?branch=master)](https://github.com/lczech/gappa/actions) --\u003e\n\u003c!-- [![Build Status](https://travis-ci.org/lczech/gappa.svg?branch=master)](https://travis-ci.org/lczech/gappa) --\u003e\n\n![gappa](/doc/logo/logo_readme.png?raw=true \"gappa\")\n\nFeatures\n-------------------\n\ngappa is a collection of commands for working with phylogenetic data.\nIts main focus are evolutionary placements of short environmental sequences on a reference phylogenetic tree.\nSuch data are typically produced by tools such as [EPA-ng](https://github.com/Pbdas/epa-ng),\n[RAxML-EPA](http://sco.h-its.org/exelixis/web/software/epa/index.html) or\n[pplacer](http://matsen.fhcrc.org/pplacer/), and usually stored in\n[jplace](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0031009) files.\n\u003c!-- It however also offers some commands for working with data such as sequences or trees. --\u003e\nSee [**the Wiki pages**](https://github.com/lczech/gappa/wiki)\nfor the full list of all subcommands and their documentation.\n\nWe 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.\n\nSetup\n-------------------\n\nThere are two ways to get gappa:\n\n1. Install it via [conda](https://anaconda.org/bioconda/gappa).\n2. Build it from source.\n\nWhile conda will only give you proper releases,\nbuilding from source will give you the latest (development) version.\nFor that, simply get it, and build it:\n\n~~~.sh\ngit clone --recursive https://github.com/lczech/gappa.git\ncd gappa\nmake\n~~~\n\nYou can also use the green \"Code\" button above or\n[click here](https://github.com/lczech/gappa/archive/master.zip) to download the source as a zip\narchive. Unpack, and call `make` in the main directory to build everything.\n\nRequirements:\n\n *  [Make](https://www.gnu.org/software/make/) and [CMake](https://cmake.org/) 3.1 or higher.\n *  A fairly up-to-date C++11 compiler, e.g.,\n    [clang++ 3.6](http://clang.llvm.org/) or [GCC 4.9](https://gcc.gnu.org/), or higher.\n\nAfter building, the executable is stored in the `bin` directory, and used as follows.\n\nUsage and Documentation\n-------------------\n\ngappa is used via its command line interface, with subcommands for each task.\nThe commands have the general structure:\n\n    gappa \u003cmodule\u003e \u003csubcommand\u003e \u003coptions\u003e\n\n\u003c!-- The modules are simply a way of organizing the commands,\nand have no [deeper meaning](https://en.wikipedia.org/wiki/42_%28answer%29). --\u003e\n\nSee [**the Wiki pages**](https://github.com/lczech/gappa/wiki)\nfor the full list of all subcommands and their documentation.\n\nFor **bug reports and feature requests** of gappa, please\n[open an issue on GitHub](https://github.com/lczech/gappa/issues).\n\nFor **user support**, please see our\n[Phylogenetic Placement Google Group](https://groups.google.com/forum/#!forum/phylogenetic-placement).\nIt is intended for discussions about phylogenetic placement,\nand for user support for our software tools, such as [EPA-ng](https://github.com/Pbdas/epa-ng),\n[gappa](https://github.com/lczech/gappa), and [genesis](https://github.com/lczech/genesis).\n\nCitation\n-------------------\n\n**To generally cite gappa, please use**\n\n\u003e Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data.\u003cbr /\u003e\n\u003e Lucas Czech, Pierre Barbera, and Alexandros Stamatakis.\u003cbr /\u003e\n\u003e Bioinformatics, 2020. https://doi.org/10.1093/bioinformatics/btaa070\u003cbr /\u003e\n\nEach 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\n](https://github.com/lczech/gappa/wiki/Citation-and-References) for a list of all references.\n\nLastly, we recommend reading our comprehensive review of the topic\n\n\u003e Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade.\u003cbr /\u003e\n\u003e Lucas Czech, Alexandros Stamatakis, Micah Dunthorn, and Pierre Barbera.\u003cbr /\u003e\n\u003e Frontiers in Bioinformatics, 2022. https://doi.org/10.3389/fbinf.2022.871393  \n\nto get an overview of phylogenetic placement and its methods.\n\nBehind the scenes\n-------------------\n\ngappa is short for Genesis Applications for Phylogenetic Placement Analysis.\nThis is because most of the work of gappa is actually performed by our [genesis](https://github.com/lczech/genesis) library.\nSee there if you are interested in the implementation details.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flczech%2Fgappa","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flczech%2Fgappa","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flczech%2Fgappa/lists"}