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Provide accessibility to the large iPTOL species tree for the target audience of molecular, cellular, and developmental biologists by enabling (a) applications that take advantage of a large species tree to interpret the functional evolution of one to many gene families, and (b) generation of hypotheses about functional shifts along branches of the species tree by simultaneous analysis of multiple reconciled gene trees.

Subgoals

NOTE: These are just some suggestions to get the ball rolling. Let's continue brainstorming them and then prioritize them based on feasibility, usefulness, etc.

1. Characterize the scaling properties of existing algorithms for tree reconciliation.

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Preliminary project milestones

NOTE: this needs to be revised once the above has been refined.