ReproPhylo: An Environment for Reproducible Phylogenomics

PLoS Computational Biology
Amir SzitenbergDavid H Lunt

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 Pyth...Continue Reading

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Citations

Jan 19, 2016·Trends in Ecology & Evolution·August GuangCasey W Dunn
Feb 28, 2016·Molecular Biology and Evolution·Jaime Huerta-CepasPeer Bork
Oct 17, 2017·Genome Biology and Evolution·Amir SzitenbergDavid H Lunt
Oct 27, 2018·Ecological Applications : a Publication of the Ecological Society of America·Stephen M Powers, Stephanie E Hampton
Aug 28, 2016·Genome Biology and Evolution·Amir SzitenbergDavid H Lunt
Jul 28, 2016·Molecular Ecology Resources·Sereina RutschmannMichael T Monaghan
Jul 18, 2018·BMC Medical Informatics and Decision Making·Kavishwar B WagholikarShawn N Murphy

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Software Mentioned

Biopython
SeqRecord
Pal2Nal
ReproPhylo Galaxy
MAFFT
Google Docs
ReproPhylo
MultipleSeqAlignment Biopython
Osiris
MIAPA

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