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Published May 26, 2023 | Version 1.3.0
Software Open

vmikk/PhyloNext: 1.3.0

Creators

  • 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

Description

PhyloNext is the automated pipeline for the analysis of phylogenetic diversity using GBIF occurrence data, species phylogenies from Open Tree of Life, and Biodiverse software.

Introduction

Current pipeline brings together two critical research data infrastructures, the Global Biodiversity Information Facility (GBIF) and Open Tree of Life (OToL), to make them more accessible to non-experts.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.

The pipeline could be launched in a cloud environment (e.g., the Microsoft Azure Cloud Computing Services, Amazon AWS Web Services, and Google Cloud Computing Services).

Pipeline summary

  1. Filtering of GBIF species occurrences for various taxonomic clades and geographic areas
  2. Removal of non-terrestrial records and spatial outliers (using density-based clustering)
  3. Preparation of phylogenetic tree (currently, only pre-constructed phylogenetic trees are available; with the update of OToL, phylogenetic trees will be downloaded automatically using API) and name-matching with GBIF species keys
  4. Spatial binning of species occurrences using Uber’s H3 system (hexagonal hierarchical spatial index)
  5. Estimation of phylogenetic diversity and endemism indices using Biodiverse program
  6. Visualization of the obtained results

User documentation: https://phylonext.github.io/

Source code: https://github.com/vmikk/PhyloNext

Notes

## 1.3.0 - [May 25, 2023] - Biodiverse updated to v4.3 Biodiverse changelog: - [Version 4.3](https://github.com/shawnlaffan/biodiverse/releases/tag/r4.3) - [Version 4.2](https://github.com/shawnlaffan/biodiverse/releases/tag/r4.2) - `Added`: `maxyear` parameter for occurrence filtering based on the upper bound of collection year

Files

vmikk/PhyloNext-1.3.0.zip

Files (14.6 MB)

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Additional details

Related works

Is supplement to
Software: https://github.com/vmikk/PhyloNext/tree/1.3.0 (URL)
Is supplemented by
Software: 10.5281/zenodo.7973798 (DOI)
Software documentation: https://phylonext.github.io/ (URL)