ReproPhylo: An Environment for Reproducible Phylogenomics

Abstract

The reproducibility of experiments is key to the scientific process, and particularly necessary for accurate reporting of analyses in data-rich fields such as phylogenomics. We present ReproPhylo, a phylogenomic analysis environment developed to ensure experimental reproducibility, to facilitate the handling of large-scale data, and to assist methodological experimentation. Reproducibility, and instantaneous repeatability, is built in to the ReproPhylo system and does not require user intervention or configuration because it stores the experimental workflow as a single, serialized Python object containing explicit provenance and environment information. This ‘single file’ approach ensures the persistence of provenance across iterations of the analysis, with changes automatically managed by the version control program Git. This file, along with a Git repository, are the primary reproducibility outputs of the program. In addition, ReproPhylo produces an extensive human-readable report and generates a comprehensive experimental archive file, both of which are suitable for submission with publications. The system facilitates thorough experimental exploration of both parameters and data. ReproPhylo is a platform independent CC0 Python module and is easily installed as a Docker image or a WinPython self-sufficient package, with a Jupyter Notebook GUI, or as a slimmer version in a Galaxy distribution.

Phylogenomics — principles, opportunities and pitfalls of big‐data phylogenetics

“…Several recommendations and guidelines to promote the best practices in reproducibility and data management in phylogenomics and bioinformatics have been proposed (Cranston et al, 2014;Magee, 2014;Debiasse & Ryan, 2019), and many tools for ensuring provenance and curation of both data and methods have been developed (e.g. Dunn, 2013;Oakley, 2014;Szitenberg, 2015).…”

discomark: nuclear marker discovery from orthologous sequences using draft genome data

“…Default parameters are the following: '-localpair -maxiterate 16 -inputorderpreservecase -quiet' (L-INS-i alignment method). We chose MAFFT as multiple alignment tool because it combines accuracy and efficiency and has been adopted widely in the scientific community (Pais et al 2014;Szitenberg et al 2015).…”

Comparative genomics of apomictic root-knot nematodes: hybridization, ploidy, and dynamic genome change

“…It should be possible to re-create all figures from these notebooks. Phylogenomic analyses made use of ReproPhylo an environment for reproducible phylogenomics [56] . Raw data is published in BioProject PRJNA340324 and genome assemblies, intermediate data transformations, and methods notebooks can be found in the manuscript's git repository: https://github.com/HullUni-bioinformatics/MIG-Phylogen omics#mig-phylogenomics de50fe4 .…”

“…The first was rooted with sequences from M. enterolobii and the second was an unrooted tree that only included sequence from MIG species. The analysis was kept reproducible with ReproPhylo [56] . Single gene datasets were aligned with the l-ins-i algorithm in MAFFT [60] and trimmed with TrimAl [61] to exclude alignment columns with more than 10% missing data.…”