Possible Use Cases for a TR Discovery Environment

The following is a list of possible iPlant Discovery Environment use cases related to gene trees, species trees and tree reconciliations:

1. Reconcile a gene tree and species tree chosen from tree databases or submitted in some standard form.
   • Entry point: gene family name or tree + taxon tree or list (tree derived from taxon list using phylomatic-like tool)
2. Show all gene and genome duplications in a gene family tree.
   • Entry point: fasta file, list of genes or exemplar gene for a gene family
3. Find all gene trees showing a duplication event at a specific point on a species tree.
   • Entry point: reference point (node) in species tree.
4. Find points on a species tree where a set of genes (e.g. all genes within a pathway or GO category) originated and/or diversified.
   • Entry point: gene sequence(s), gene name(s) pathway, GO annotation
5. Find all gene trees with homeologs for a particular taxon and scan trees for evidence of functional divergence between homeologous genes.
   • Entry point:taxon name
6. Re-estimate species tree (DupTree) given a specified subset of all gene trees.
   • Entry point: list of genes or gene families
7. Show all gene trees with a specified pattern of taxon sampling, gene duplication and/or gene retension.
   • Entry point: tree description
8. Link to natural history information on each taxon in species tree.
   • Geographic distribution
   • Habit and Habitat type
   • Medicinal or Agricultural use
   • Other anthropogenic uses
   • Entry point: taxon name
9. Host taxon information wiki?
   • Entry point:Taxon name
10. Show most highly expressed genes in a taxon and then place these genes within gene trees. Do related genes show similar expression levels/patterns?
    • RNA source tissue?
    • Entry point: taxon/taxa name(s)
11. Linkout to metabolic pathway databases from gene identifiers.
    • Entry point: genes may be shown in context of gene tree.
12. Show sampled gene copy number for all taxa
    • Entry point: gene family identifier
13. It would be nice to link into a discovery environment through NCBI (genes, species...), Web Tree of Life (taxon), APweb (taxon) or other high profile sites.
14. Show inferred timing of genome duplication events on species tree.
15. Show estimated divergence times
    • Entry point: gene tree or species tree
16. Organize gene set into PlantTribes
    • Entry point: fasta file with a large set of sequences
17. Gene/gene family annotation wiki?
    • Entry point: Gene sequence, annotation term or ID

I've started prioritizing this list here: Use case prioritization (tjv) - Todd