Published May 26, 2023 | Version 1.3.0
Software Open

PhyloNext Pipeline - Docker and Singularity Image Archives

  • 1. Institute of Ecology and Earth Sciences, University of Tartu, Estonia
  • 2. Natural History Museum, University of Tartu, Estonia
  • 3. Earth and Sustainability Science Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
  • 4. Global Biodiversity Information Facility, Copenhagen, Denmark
  • 5. School of Natural Sciences, University of California, Merced, USA
  • 6. Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, USA


PhyloNext is a pipeline for phylogenetic diversity analysis of GBIF-mediated data.

Source code at GitHub:

User documentation:


This repository contains Docker and Singularity image archives of the PhyloNext pipeline, which facilitate the use and reproducibility of computational phylogenetics and biodiversity analyses. The images encapsulate all the software dependencies used by PhyloNext, compartmentalized into three distinct containers:

  1. rarrow: This container integrates the statistical programming language R and Apache Arrow. This combination provides a powerful set of tools for data analysis and manipulation in PhyloNext, utilizing Arrow's columnar format for efficient data analytics operations.

  2. biodiverse: The biodiverse container comprises Biodiverse, a tool for the spatial analysis of diversity (Laffan et al., 2010, DOI:10.1111/j.1600-0587.2010.06237.x;, and Perl, a high-level, general-purpose, interpreted, dynamic programming language. Biodiverse, powered by Perl, allows users to analyze spatial patterns of diversity using indices based on taxon, phylogenetic, trait and matrix-based (e.g. genetic, distance) variations.

  3. opentree: The opentree container integrates the Open Tree of Life (OToL) resource, a comprehensive, dynamic and digitally-available tree of life by synthesizing published phylogenetic trees, and Python, a widely used high-level programming language. This enables PhyloNext to incorporate and manipulate phylogenetic data from OpenTree using Python's vast suite of libraries and tools.

Docker and Singularity definition files used to create containers are available at:

All images are hosted on



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