Holmes Lab: end-of-series reference index

putting the summer pointers here before everything becomes a mystery folder. keep commands, seeds, versions, control files... a plot alone is not going to help me rerun anything.

• dated record: August 11 is the final summer meeting in the shared log. The entry supplies no experiment configuration or new result, so it serves as a navigation marker.

• technical material to preserve from the summer: the joint alignment/tree/ancestral-state model; pairHMM and indel readings; the EvolDeeds scoring/uncertainty brainstorm; and the ReconBench simulation/evaluation pipeline. The August 4 entry records a presentation on EvolDeeds and EvolMoves, but does not provide its technical slides in the meeting log.

• review checklist: retain runnable repository revision, simulation control files, tool versions, seeds, parameter tables, run logs and posterior-summary choices. Keep proposal settings separate from settings actually written to a runtime manifest.

• follow-on sources: the 2025 evaluation report and September terminal log contain implementation details and failures absent from the meeting summary. Those deserve their own reference notes rather than being assigned retroactively to the final meeting date.

My tree-search notes: NNI, SPR, TBR, and consensus.