standards > model/format > DOI:10.25504/FAIRsharing.3mprr8


ready XML for evolutionary biology and comparative genomics.

Abbreviation: phyloXML


General Information
PhyloXML is an XML language designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elements for commonly used features, such as taxonomic information, gene names and identifiers, branch lengths, support values, and gene duplication and speciation events.



How to cite this record FAIRsharing.org: phyloXML; XML for evolutionary biology and comparative genomics.; DOI: https://doi.org/10.25504/FAIRsharing.3mprr8; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Nov 27 2020 8:21 p.m.


Record updated: March 15, 2018, 10:12 a.m. by The FAIRsharing Team.

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Publications

phyloXML: XML for evolutionary biology and comparative genomics.

Han MV,Zmasek CM
BMC Bioinformatics 2009

View Paper (PubMed) View Publication

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Models and Formats

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Related Databases (3)
Integrated Microbial Genomes And Microbiomes
The Integrated Microbial Genomes (IMG/M) aims to support the annotation, analysis and distribution of microbial genome and microbiome datasets sequenced at DOE's Joint Genome Institute (JGI). It also serves as a community resource for analysis and annotation of genome and metagenome datasets in a comprehensive comparative context. The IMG data warehouse integrates genome and metagenome datasets provided by IMG users with a set of publicly available genome and metagenome datasets. IMG/M is also open to scientists worldwide for the annotation, analysis, and distribution of their own genome and microbiome datasets, as long as they agree with the IMG/M data release policy and follow the metadata requirements for integrating data into IMG/M.

Virus Pathogen Database and Analysis Resource
The Virus Pathogen Database and Analysis Resource (ViPR) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Centers (BRC) program. ViPR captures various types of information, including sequence records, gene and protein annotations, 3D protein structures, immune epitope locations, clinical and surveillance metadata and novel data derived from comparative genomics analysis. The database is available without charge as a service to the virology research community to help facilitate the development of diagnostics, prophylactics and therapeutics for priority pathogens and other viruses.

GreenPhylDB: A phylogenomic database for plant comparative genomics
GreenPhylDB comprises 37 full genomes from the major phylum of plant evolution. Clustering of these genomes was performed to define a consistent and extensive set of homeomorphic plant families.

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