ArticleBMC bioinformatics2009
phyloXML: XML for evolutionary biology and comparative genomics.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 297 papers.
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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.
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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
297 citing papers in PubMed.
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- New viral sequences and endogenous viral elements (EVE) in world-wide populations of Trioza erytreae, the African citrus psyllid.Virus research · 2026Article
- An enzyme's metal preference evolves through redox modulation driven by the cofactor's secondary coordination sphere.Molecular biology and evolution · 2026Article
- PhyloScape: interactive and scalable visualization platform for phylogenetic trees.BMC bioinformatics · 2025Article
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- Discovering the dynamics of peach fruit mycobiome throughout fruit development season by high-throughput sequencing.Scientific reports · 2025Article
- Faithful Interpretation of Protein Structures through Weighted Persistent Homology Improves Evolutionary Distance Estimation.Molecular biology and evolution · 2025Article
- Cloning and Recombinant Expression of the Caspase-Activated DNase Orthologous Gene ofBioMed research international · 2025Article
- Genetic and neuro-epigenetic effects of divergent artificial selection for feather pecking behaviour in chickens.BMC genomics · 2024Article
- Assembly, Annotation, and Comparative Analysis of Mitochondrial Genomes inInternational journal of molecular sciences · 2024Article
- Novel, active, and uncultured hydrocarbon-degrading microbes in the ocean.Applied and environmental microbiology · 2024Article
- Phylogenomic Analyses of Three Distinct Lineages UnitingMicroorganisms · 2024Article
- Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool.Nucleic acids research · 2024Article
- The venom and telopodal defence systems of the centipede Lithobius forficatus are functionally convergent serial homologues.BMC biology · 2024Article
- PhyloJS: Bridging phylogenetics and web development with a JavaScript utility library.Ecology and evolution · 2024Article
- Molecular Genomic Analyses ofMicroorganisms · 2024Article
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- Horizontal acquisition of a DNA ligase improves DNA damage tolerance in eukaryotes.Nature communications · 2023Article
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237 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
backgroundEvolutionary trees are central to a wide range of biological studies. In many of these studies, tree nodes and branches need to be associated (or annotated) with various attributes. For example, in studies concerned with organismal relationships, tree nodes are associated with taxonomic names, whereas tree branches have lengths and oftentimes support values. Gene trees used in comparative genomics or phylogenomics are usually annotated with taxonomic information, genome-related data, such as gene names and functional annotations, as well as events such as gene duplications, speciations, or exon shufflings, combined with information related to the evolutionary tree itself. The data standards currently used for evolutionary trees have limited capacities to incorporate such annotations of different data types.
resultsWe developed a XML language, named phyloXML, for describing evolutionary trees, as well as various associated data items. PhyloXML provides elements for commonly used items, such as branch lengths, support values, taxonomic names, and gene names and identifiers. By using "property" elements, phyloXML can be adapted to novel and unforeseen use cases. We also developed various software tools for reading, writing, conversion, and visualization of phyloXML formatted data.
conclusionPhyloXML is an XML language defined by a complete schema in XSD that allows storing and exchanging the structures of evolutionary trees as well as associated data. More information about phyloXML itself, the XSD schema, as well as tools implementing and supporting phyloXML, is available at http://www.phyloxml.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.