Genesis and Gappa: Processing, Analyzing and Visualizing Phylogenetic (Placement) Data

Abstract:

The ever increasing amount of genomic and meta-genomic sequence data has transformed biology into a data-driven and compute-intensive discipline. Hence, there is a need for efficient algorithms and scalable implementations thereof for analysing such data.

We present GENESIS, a library for working with phylogenetic data, and GAPPA, an accompanying command line tool for conducting typical analyses on such data. While our tools primarily target phylogenetic trees and phylogenetic placements, they also offer a plethora of functions for handling genetic sequences, taxonomies, and other relevant data types.

The tools aim at improved usability at the production stage (conducting data analyses) as well as the development stage (rapid prototyping): The modular interface of GENESIS simplifies numerous standard high-level tasks and analyses, while allowing for low-level customization at the same time. Our implementation relies on modern, multi-threaded C++11, and is substantially more com-putationally efficient than analogous tools. We already employed the core GENESIS library in several of our tools and publications, thereby proving its flexibility and utility. GENESIS and GAPPA are freely available under GPLv3 at http://github.com/lczech/genesis and http://github.com/lczech/gappa.

SEEK ID: https://publications.h-its.org/publications/480

DOI: 10.1101/647958

Research Groups: Computational Molecular Evolution

Publication type: Journal

Journal: bioRxiv

Citation: biorxiv;647958v3,[Preprint]

Date Published: 28th May 2019

Registered Mode: by DOI

Authors: Lucas Czech, Pierre Barbera, Alexandros Stamatakis

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Citation
Czech, L., Barbera, P., & Stamatakis, A. (2019). Genesis and Gappa: Processing, Analyzing and Visualizing Phylogenetic (Placement) Data. In []. Cold Spring Harbor Laboratory. https://doi.org/10.1101/647958
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Created: 22nd Oct 2019 at 11:16

Last updated: 5th Mar 2024 at 21:23

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