phyloXML: XML for evolutionary biology and comparative genomics

By Mira V. Han, Christian M. Zmasek. BMC Bioinformatics, 2009

560 citations recorded by the source corpus.

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.

Subfields: Ecology, Evolution, Behavior and Systematics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/e9c68b4983f5f0bc12c8cb6c5402521009267e7a

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Citations in the corpus

PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics (2017, methodology): “The previous PLAZA versions relied on the externally developed software tool Archaeopteryx (previously ATV) (9) to display these phylogenetic trees.”
Auto-antibodies against type I IFNs in patients with life-threatening COVID-19 (2020, unknown): “The tree was then visualized ( 38 ).”
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees (2016, methodology): “iTOL works with commonly used phylogenetic tree formats, Newick, Nexus (9) and phyloXML (10).”
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation (2021, methodology): “iTOL supports commonly used phylogenetic tree formats such as Newick, Nexus (9) and phyloXML (10).”
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees (2023, methodology): “…layer manager and a project manager. tvBOT supports se v eral phylogenetic tree formats as input, including Ne wick, Ne xus ( 8 ) and phyloXML ( 9 ), which can be displayed as phylograms (Figure 2 ) and cladograms (Supplementary Figure S1), each in r ectangular, cir cular or unrooted la y out…”
Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood (2011, unknown): “Finally, the Web server also offers a JAVA-based result visualization tool that uses the Archeopteryx framework (Han and Zmasek 2009) and provides a simple visualization of the read distribution over the RT.”
ViPR: an open bioinformatics database and analysis resource for virology research (2011, methodology): “Phylogenetic tree reconstructions can then be saved in the Workbench or downloaded in either Newick or phyloXML format (31).”
Compact graphical representation of phylogenetic data and metadata with GraPhlAn (2015, methodology): “GraPhlAn provides separate visualization options for trees (thus potentially unannotated) and their annotations, the latter of which (the annotation module) attaches metadata properties using the PhyloXML format ( Han & Zmasek, 2009 ).”
Interactive Tree Of Life (iTOL) v4: recent updates and new developments (2019, methodology): “iTOL supports commonly used phylogenetic tree formats: Newick, Nexus (9) and phyloXML (10).”
EvolView, an online tool for visualizing, annotating and managing phylogenetic trees (2012, methodology): “It takes phylogenetic trees in several formats as input, including Newick/ Phylip, Nexus (17), Nhx and PhyloXML (18) formats.”
aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity (2013, methodology): “The resulting tree is intended to roughly visualize the tree-like relationship for even large numbers of sequences and to provide visual guidance for the next steps, and is displayed with a Java applet version of the Archaeopteryx phylogenetic tree visualization and analysis tool (19,20).”
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy (2011, background): “Recently proposed new tree format, phyloXML (9) is also supported.”
IMG: the integrated microbial genomes database and comparative analysis system (2011, methodology): “org/archaeopteryx/), which uses phyloXML for data exchange (30).”
TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes (2021, unknown): “The TYGS platform was similarly augmented with a REST API to allow users to download tabular results in the open interchange format JSON, phylogenetic results in either PhyloXML (36) or Newick format and scientific citations in BibTex format.”
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree (2010, methodology): “The richest visualizations make use of the phyloXML format [49], which can be viewed using the freely available Archaeopteryx [32] Java software.”