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PRO/PROEVO http://www.bioontology.org/wiki/index.php/PRO protein evolutionary families, multiple endproducts of genes in development
Protein Ontology http://proteinontology.info/ protein structure, function implementation
RnaO http://roc.bgsu.edu/ RNA sequence, structure, motifs, alignments in development
GO implementation
SO implementation
PATO http://www.bioontology.org/wiki/index.php/PATO phenotypic and trait ontology implementation
MAO http://bips.u-strasbg.fr/LBGI/MAO/mao.html multiple alignments of DNA,
RNA and protein sequences and structures implementation
NCBI Taxonomy http://www.ncbi.nlm.nih.gov/Taxonomy/ Organismal classification,
genetic code used widely
Data formats, database schemas
NCBI data model http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/DATAMODL.HTML sequences, alignments, annotations used at NCBI
NEXUS format Maddison, et al., 1997 character data, trees, assumptions, sets, notes used widely
NeXML https://www.nescent.org/wg_evoinfo/Future_Data_Exchange_Standard character data, trees, models, meta-info in development
pPOD processing of data related to phylogenetic analysis workflows in development
CHADO http://www.gmod.org/wiki/index.php/Schema sequence, genotypes, phenotypes, phylogenies used in GMOD
TreeBase http://www.treebase.org character data, trees, meta-info on analyses in use
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