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README.md

genesis

A library for working with phylogenetic data.

Build Status License Language

Features

Genesis is a C++ library for working with phylogenetic data. A 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.

Some of the features of genesis:

  • Placements
    • Read, manipulate and write jplace files.
    • Manipulate placement data: extract, filter, merge, and much more.
    • Calculate distance measures (e.g., KR distance, EDPL).
    • Run analyses like k-means Clustering, Squash Clustering, Edge PCA.
    • Visualize aspects like read abundances or correlation with meta-data on the branches of the tree.
  • Trees
    • Read, annotate and write trees in various formats.
    • Versatile tree data structure that can store any data on the edges and nodes.
    • Easily iterate trees with different policies (e.g., postorder, preorder).
    • Directly draw trees with colored branches to SVG files.
  • Sequences and Taxonomies
    • Read, filter, manipulate and write sequences in fasta and phylip format.
    • Calculate consensus sequences with different methods.
    • Work with taxonomic paths and build a taxonomic hierarchy.
  • Utilities
    • Math tools (matrices, histograms, statistics functions etc)
    • Color support (color lists, gradients etc, for making colored trees)
    • Various supportive file formats (bmp, csv, json, xml and more)

This is just an overview of the more prominent features. See the API reference for more.

Setup and Getting Started

For download and build instructions, see Setup.

You futhermore find all the information for getting started with genesis in the documentation. It contains a user manual with setup instructions and tutorials, as well as the full API reference.

For user support, please see our Phylogenetic Placement Google Group. It is intended for discussions about phylogenetic placement, and for user support for our software tools. You can also find support for EPA-ng and Gappa there.

For bug reports and feature requests, please open an issue on our GitHub page.

Showcase

A focus point of the toolkit is to work with phylogenetic placements. The following figure summarized the placement position of 7.5 mio short reads on a reference tree with 190 taxa. The colour code indicates the number of reads placed on each branch.

Phylogenetic tree with coloured branches.