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

ready XML for evolutionary biology and comparative genomics.


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: phyloXML; XML for evolutionary biology and comparative genomics.; DOI:; Last edited: March 15, 2018, 11:53 a.m.; Last accessed: Mar 24 2018 10:20 a.m.

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

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phyloXML: XML for evolutionary biology and comparative genomics.

Han MV,Zmasek CM
BMC Bioinformatics 2009

View Paper (PubMed) View Paper (DOI)

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Models and Formats

Implementing Databases (3)
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.

Integrated Microbial Genomes
The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses.

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