Citation and References

Citation

When using gappa commands, they will output the necessary citations for the command.

To generally cite gappa, please use

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

Each command also prints out the relevant references. Then, the command gappa tools citation can be used to obtain details on those references. See also below for a list of them.

References of the Methods

Many commands in gappa are implementations of our novel methods as described in

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

At the same time, it offers some commands that are also implemented in the excellent guppy tool. When using these commands, please also cite

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree.
Frederick A Matsen, Robin B Kodner, and Virginia Armbrust.
BMC Bioinformatics, 2010. https://doi.org/10.1186/1471-2105-11-538

However, being written in C++, our gappa is much faster and needs less memory for most of the tasks.

Furthermore, some methods build heavily on previous work of others. When using the KR distance computation, please cite

The phylogenetic Kantorovich-Rubinstein metric for environmental sequence samples.
Steven Evans and Frederick Matsen.
Journal of the Royal Statistical Society, 2012. https://doi.org/10.1111/j.1467-9868.2011.01018.x

The Placement-Factorization heavily borrows from methods presented in

Phylogenetic Factorization of Compositional Data Yields Lineage-Level Associations in Microbiome Datasets.
Alex Washburne, Justin Silverman, Jonathan Leff, Dominic Bennett, John Darcy, Sayan Mukherjee, Noah Fierer, and Lawrence David.
PeerJ, 2017. https://doi.org/10.7717/peerj.2969

The respective commands in gappa also output information on which references need to be cited.

Further References

Lastly, we recommend reading our comprehensive review of the topic

Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade.
Lucas Czech, Alexandros Stamatakis, Micah Dunthorn, and Pierre Barbera.
Frontiers in Bioinformatics, 2022. https://doi.org/10.3389/fbinf.2022.871393

to get an overview of phylogenetic placement and its methods.