A library for working with phylogenetic and population genetic data.
Genesis is a C++ library for working with phylogenetic and population genetic data:
jplace
files from phylogenetic placement analyses.sam
/bam
/cram
, pileup
, sync
, and vcf
, as well as auxiliary formats such as gff
/gtf
, bim
/map
, and bed
.fasta
, fastq
, and phylip
format.This is just an overview of the more prominent features. See the API reference for more.
Genesis is a library that is intended for researchers and developers who want to build their own tools and methods, or run their own custom analyses. If you are simply interested in analyzing your data with our methods, have a look at our command line tool Gappa for many common phylogenetic placement analyses.
For download and build instructions, see Setup.
You furthermore 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 bug reports and feature requests of genesis, please open an issue on our GitHub page.
For user support of the phylogenetic placement parts of the library, please see our Phylogenetic Placement Google Group. It is intended for discussions about phylogenetic placement, and for user support for our software tools, such as EPA-ng and Gappa.
A focus point of the library 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 color code indicates the number of reads placed on each branch.
This and other methods are presented in our manuscripts
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
See there for more on what Genesis can do.
When using Genesis, please cite
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
Also, see Gappa for our command line tool to run your own analyses.