Allows users to reduce a SpeciesTree to match the genomes in a GenomeSet.
This App allows the user to trim a Species Tree to just include the Genomes that are found in a GenomeSet. The trimmed tree is then offered as a static image and provided as links to download the image in PNG and PDF formats. One can also download a file containing the NEWICK representation of the tree (with identifiers or labels). There is also button ( View report in separate window ) and a link to open a new web page with just the image of the tree.
Team members who developed & deployed algorithm in KBase: Dylan Chivian. For questions, please contact us.
Related Publications
- Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163 , https://www.nature.com/articles/nbt.4163
App Specification:
https://github.com/kbaseapps/kb_phylogenomics/tree/aed8564fcf4c6e8a3e94f6546715496e6fffbd84/ui/narrative/methods/trim_speciestree_to_genomesetModule Commit: aed8564fcf4c6e8a3e94f6546715496e6fffbd84