| 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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