{"id":17119730,"url":"https://github.com/lczech/genesis","last_synced_at":"2025-10-26T17:10:46.533Z","repository":{"id":22363001,"uuid":"25699180","full_name":"lczech/genesis","owner":"lczech","description":"A library for working with phylogenetic and population genetic 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\"genesis\")](http://genesis-lib.org/)\n\nA library for working with phylogenetic and population genetic data.\n\n\u003c!-- [![CI](https://github.com/lczech/genesis/workflows/CI/badge.svg?branch=master)](https://github.com/lczech/genesis/actions) --\u003e\n[![CI](https://github.com/lczech/genesis/actions/workflows/ci.yaml/badge.svg)](https://github.com/lczech/genesis/actions/workflows/ci.yaml)\n[![Softwipe Score](https://img.shields.io/badge/softwipe-9.0/10.0-brightgreen)](https://github.com/adrianzap/softwipe/wiki/Code-Quality-Benchmark)\n[![License](https://img.shields.io/badge/license-GPLv3-blue.svg)](http://www.gnu.org/licenses/gpl.html)\n![Language](https://img.shields.io/badge/language-C%2B%2B11-lightgrey.svg)\n[![Platforms](https://img.shields.io/conda/pn/bioconda/gappa)](https://anaconda.org/bioconda/gappa)\n\u003cbr /\u003e\n[![Release](https://img.shields.io/github/v/release/lczech/genesis.svg)](https://github.com/lczech/genesis/releases)\n[![DOI](https://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbtaa070-blue)](https://doi.org/10.1093/bioinformatics/btaa070)\n\u003c!-- [![Build Status](https://travis-ci.org/lczech/genesis.svg?branch=master)](https://travis-ci.org/lczech/genesis) --\u003e\n\u003c!--![Language](https://img.shields.io/badge/language-python-lightgrey.svg)--\u003e\n\nFeatures\n-------------------\n\nGenesis is a C++ library for working with phylogenetic and population genetic data:\n\u003c!-- Some of the features of genesis: --\u003e\n\n *  **Trees**\n     *  Read, annotate and write trees in various formats.\n     *  Versatile tree data structure that can store any data on the edges and nodes.\n     *  Easily iterate trees with different policies (e.g., postorder, preorder).\n     *  Directly draw trees with colored branches to SVG files.\n *  **Placements**\n     *  Read, manipulate and write `jplace` files from phylogenetic placement analyses.\n     *  Manipulate placement data: extract, filter, merge, and much more.\n     *  Calculate distance measures (e.g., KR distance, EDPL).\n     *  Run analyses like k-means Clustering, Squash Clustering, Edge PCA.\n     *  Visualize aspects like read abundances or correlation with meta-data on the branches of the tree.\n *  **Populations**\n     *  Read and work with genome mapping and variant formats such as `sam`/`bam`/`cram`, `pileup`, `sync`, and `vcf`, as well as auxiliary formats such as `gff`/`gtf`, `bim`/`map`, and `bed`.\n     *  Iterate positions in a genome, individually or in different types of windows.\n     *  Compute statistics such as Tajima's D and F_ST for pool sequencing data.\n *  **Sequences** and **Taxonomies**\n     *  Read, filter, manipulate and write sequences in `fasta`, `fastq`, and `phylip` format.\n     *  Calculate consensus sequences with different methods.\n     *  Work with taxonomic paths and build a taxonomic hierarchy.\n *  **Utilities**\n     *  Math tools (matrices, histograms, statistics functions etc)\n     *  Color support (color lists, gradients etc, for making colored trees)\n     *  Various supportive file formats (bmp, csv, json, xml and more)\n\nThis is just an overview of the more prominent features.\nSee the [API reference](http://doc.genesis-lib.org/namespaces.html) for more.\n\nGenesis is a library that is intended for researchers and developers who want to build their own\ntools and methods, or run their own custom analyses. If you are simply interested in analyzing your\ndata with our methods, have a look at our command line tool [Gappa](https://github.com/lczech/gappa)\nfor many common phylogenetic placement analyses.\n\n\u003c!-- A main focus are evolutionary placements of short environmental sequences\non a reference phylogenetic tree.\nSuch data is typically produced by tools like [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 `jplace` files. --\u003e\n\nSetup and Getting Started\n-------------------\n\n\u003c!--\nThe functionality of genesis can be used in two ways:\n\n *  As a C++ library.\n *  As a Python module.\n--\u003e\n\nFor download and build instructions, see **[Setup](http://doc.genesis-lib.org/setup.html)**.\n\nYou furthermore find all the information for getting started with genesis in the\n**[documentation](http://doc.genesis-lib.org/)**.\nIt contains a user manual with setup instructions and tutorials, as well as the full API reference.\n\nFor **bug reports and feature requests** of genesis, please\n[open an issue on our GitHub page](https://github.com/lczech/genesis/issues).\n\nFor **user support** of the phylogenetic placement parts of the library, 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)\nand [Gappa](https://github.com/lczech/gappa).\n\nShowcases\n-------------------\n\nA focus point of the library is to work with phylogenetic placements.\nThe following figure summarized the placement position of 7.5 mio short reads on a\nreference tree with 190 taxa. The color code indicates the number of reads placed\non each branch.\n\n![Phylogenetic tree with coloured branches.](/doc/png/placement/visualize_placements.png?raw=true \"Phylogenetic tree with coloured branches.\")\n\nThis and other methods are presented in our manuscripts\n\n\u003e Methods for Inference of Automatic Reference Phylogenies and Multilevel Phylogenetic Placement.\u003cbr /\u003e\n\u003e Lucas Czech, Pierre Barbera, and Alexandros Stamatakis.\u003cbr /\u003e\n\u003e Bioinformatics, 2018. https://doi.org/10.1093/bioinformatics/bty767\u003cbr /\u003e\n\u003e \u003c!-- bioRxiv, 2018. https://doi.org/10.1101/299792 --\u003e\n\nand\n\n\u003e Scalable Methods for Analyzing and Visualizing Phylogenetic Placement of Metagenomic Samples.\u003cbr /\u003e\n\u003e Lucas Czech and Alexandros Stamatakis.\u003cbr /\u003e\n\u003e PLOS One, 2019. https://doi.org/10.1371/journal.pone.0217050\u003cbr /\u003e\n\u003e \u003c!-- bioRxiv, 2019. https://doi.org/10.1101/346353 --\u003e\n\nSee there for more on what Genesis can do.\n\nCitation\n-------------------\n\nWhen using Genesis, please cite\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\nAlso, see [Gappa](https://github.com/lczech/gappa) for our command line tool to run your own analyses.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flczech%2Fgenesis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flczech%2Fgenesis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flczech%2Fgenesis/lists"}