TreeGenes
Public server: | TreeGenes Galaxy |
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Scope: | Domain specific |
Summary: | TreeGenes integrates genotype, phenotype, and environmental data that can be processed for association mapping and landscape genomics, with a focus on forest trees. This functionality is provided by Tripal Galaxy, a module for Tripal that provides seamless support for running Galaxy workflows directly in the site. Users can analyze data provided by TreeGenes or their own. |
comments
TreeGenes is utilizing the Tripal Galaxy API in order to provide seamless Galaxy workflow support to users on the site. Examples currently in development
- CartograTree: Web-based map-driven module to provide association and landscape genomics. Uses Sambada
- Orthoquery: Module to assess and visualize gene family evolution. Uses tools: VSEARCH, OrthoFinder, Diamond and TransDecoder
user support
Accounts can be requested through the TreeGenes site
quotas
Anonymous access and account creation are goth supported.
citations
Growing and cultivating the forest genomics database, TreeGenes, Taylor Falk, Nic Herndon, Emily Grau, Sean Buehler, Peter Richter, Sumaira Zaman, Eliza M Baker, Risharde Ramnath, Stephen Ficklin, Margaret Staton, Frank A Feltus, Sook Jung, Doreen Main, Jill L Wegrzyn. Database, Volume 2018, 1 January 2018, bay084, doi: 10.1093/database/bay084
- Beyond Search and Display – Analyze Tripal Data with CartograTree, by Sean Buehler, presented at Plant and Animal Genome XXVII (PAG 2019)
- TreeGenes tagged publications in the Galaxy Publication library
sponsors
Department of Ecology and Evolutionary Biology, University of Connecticut
- Department of Horticulture, Washington State University
- Department of Entomology and Plant Pathology, University of Tennessee
- Department of Genetics and Biochemistry, Clemson University