Repository details
The Adaptive Evolution Database
Name of repository
The Adaptive Evolution Database
Additional name(s)
- TAED
Repository URL
Description
TAED is a database of phylogenetically indexed gene families. It contains multiple sequence alignments from MAFFT1, maximum likelihood phylogenetic trees from PhyML2, bootstrap values for each node, dN/dS ratios for each lineage from the free ratios model in PAML3, and labels for each node of speciation or duplication from gene tree/species tree reconciliation using SoftParsMap4. The phylogenetic indexing enables simultaneous viewing of lineages with high dN/dS that occurred along the same species tree branches. Resources from the Protein Data Bank (PDB) and the Kyoto Encyclopedia of Genes and Genomes (KEGG)5, have been incorporated into the TAED analysis to detect substitutions along each branch within the phylogenetic tree and to assess selection within pathways.
Contact
- daliberles@temple.edu
Content type(s)
Keyword(s)
Persistent identifier(s) of the repository
- RRID:nif-0000-03533
- RRID:SCR_006930
Repository size
143.806 completed protein families; 3.185.986 proteins; 3.214 species
Repository type(s)
- disciplinary
Mission statement for designated community
Research data repository language(s)
- English
Data and/or service provider
- data provider
Institution name
Additional name(s)
- IGEM
Country
Type(s) of responsibility
- general
Type of institution
non-profit
Start date of responsibility
2016
Institution name
Identifier(s)
- ROR:021nxhr62
Contact(s)
Country
Type(s) of responsibility
- funding
Type of institution
non-profit
Start date of responsibility
2016
Institution name
Additional name(s)
- CCGG
Country
Type(s) of responsibility
- technical
Type of institution
non-profit
Start date of responsibility
2016
Institution name
Contact(s)
- daliberles@temple.edu
Country
Type(s) of responsibility
- general
Type of institution
non-profit
Policies (3)
Policy Name
Policy Name
Policy Name
Database access
Type of access to research data repository
open
Data access (1)
Type of access to data
open
Data licenses (2)
DataLicense
DataLicense
Data upload (1)
Type of data upload
closed
Cite this re3data.org record:
re3data.org: The Adaptive Evolution Database; editing status 2022-12-19; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DF5W last accessed: 2024-04-20- Current projects
- EOSC FAIR-IMPACT
- re3data COREF
-
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- Cite this service: re3data.org - Registry of Research Data Repositories. https://doi.org/10.17616/R3D last accessed: 2024-04-20
