ArticleBMC bioinformatics2012
Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython.
Article in BMC bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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Who cites it
88 citing papers in PubMed.
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- Oatk: a de novo assembly tool for complex plant organelle genomes.Genome biology · 2025Article
- Opposing roles of pseudokinases NRBP1 and NRBP2 in regulating L1 retrotransposition.Nature communications · 2025Article
- Labels as a feature: Network homophily for systematically annotating human GPCR drug-target interactions.Nature communications · 2025Article
- OGU: A Toolbox for Better Utilising Organelle Genomic Data.Molecular ecology resources · 2025Article
- Simplifying and Characterizing DAGs and Phylogenetic Networks via Least Common Ancestor Constraints.Bulletin of mathematical biology · 2025Article
- Unravelling genomic drivers of speciation in Musa through genome assemblies of wild banana ancestors.Nature communications · 2025Article
- DEFGermplasm: a comprehensive digital platform for forest genomic and phenotype data integration.Forestry research · 2025Article
- Visualizing metagenomic and metatranscriptomic data: A comprehensive review.Computational and structural biotechnology journal · 2024Review
28 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOngoing innovation in phylogenetics and evolutionary biology has been accompanied by a proliferation of software tools, data formats, analytical techniques and web servers. This brings with it the challenge of integrating phylogenetic and other related biological data found in a wide variety of formats, and underlines the need for reusable software that can read, manipulate and transform this information into the various forms required to build computational pipelines.
resultsWe built a Python software library for working with phylogenetic data that is tightly integrated with Biopython, a broad-ranging toolkit for computational biology. Our library, Bio.Phylo, is highly interoperable with existing libraries, tools and standards, and is capable of parsing common file formats for phylogenetic trees, performing basic transformations and manipulations, attaching rich annotations, and visualizing trees. We unified the modules for working with the standard file formats Newick, NEXUS and phyloXML behind a consistent and simple API, providing a common set of functionality independent of the data source.
conclusionsBio.Phylo meets a growing need in bioinformatics for working with heterogeneous types of phylogenetic data. By supporting interoperability with multiple file formats and leveraging existing Biopython features, this library simplifies the construction of phylogenetic workflows. We also provide examples of the benefits of building a community around a shared open-source project. Bio.Phylo is included with Biopython, available through the Biopython website, http://biopython.org.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.