ArticleBMC bioinformatics2011
BIO::Phylo-phyloinformatic analysis using perl.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
27 citing papers in PubMed.
- Core genome expansion inIranian journal of microbiology · 2025Article
- Unraveling Epistatic Interactions Between Sites Under Drug-Dependent Selection in the Mycobacterium tuberculosis Genome.Molecular biology and evolution · 2025Article
- Article
- The Generalized Robinson-Foulds Distance for Phylogenetic Trees.Journal of computational biology : a journal of computational molecular cell biology · 2021Article
- Episodic evolution of coadapted sets of amino acid sites in mitochondrial proteins.PLoS genetics · 2021Article
- Methods to Identify and Study the Evolution of Pseudogenes Using a Phylogenetic Approach.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Article
- BioHackathon 2015: Semantics of data for life sciences and reproducible research.F1000Research · 2020Article
- JPhyloIO: a Java library for event-based reading and writing of different phylogenetic file formats through a common interface.BMC bioinformatics · 2019Article
- Lytic xylan oxidases from wood-decay fungi unlock biomass degradation.Nature chemical biology · 2018Article
- A Comparative Analysis of the Lyve-SET Phylogenomics Pipeline for Genomic Epidemiology of Foodborne Pathogens.Frontiers in microbiology · 2017Article
- Species-Level Para- and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in European Lepidoptera.Systematic biology · 2016Article
- ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data.Molecular biology and evolution · 2016Article
- Coordinated Evolution of Influenza A Surface Proteins.PLoS genetics · 2015Article
- Pan-vertebrate comparative genomics unmasks retrovirus macroevolution.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction.Microbiome · 2014Article
- Intrasubtype reassortments cause adaptive amino acid replacements in H3N2 influenza genes.PLoS genetics · 2014Article
- Broad-scale phylogenomics provides insights into retrovirus-host evolution.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats.Bioinformatics (Oxford, England) · 2013Article
- Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.BMC bioinformatics · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPhyloinformatic analyses involve large amounts of data and metadata of complex structure. Collecting, processing, analyzing, visualizing and summarizing these data and metadata should be done in steps that can be automated and reproduced. This requires flexible, modular toolkits that can represent, manipulate and persist phylogenetic data and metadata as objects with programmable interfaces.
resultsThis paper presents Bio::Phylo, a Perl5 toolkit for phyloinformatic analysis. It implements classes and methods that are compatible with the well-known BioPerl toolkit, but is independent from it (making it easy to install) and features a richer API and a data model that is better able to manage the complex relationships between different fundamental data and metadata objects in phylogenetics. It supports commonly used file formats for phylogenetic data including the novel NeXML standard, which allows rich annotations of phylogenetic data to be stored and shared. Bio::Phylo can interact with BioPerl, thereby giving access to the file formats that BioPerl supports. Many methods for data simulation, transformation and manipulation, the analysis of tree shape, and tree visualization are provided.
conclusionsBio::Phylo is composed of 59 richly documented Perl5 modules. It has been deployed successfully on a variety of computer architectures (including various Linux distributions, Mac OS X versions, Windows, Cygwin and UNIX-like systems). It is available as open source (GPL) software from http://search.cpan.org/dist/Bio-Phylo.
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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.