Holmes Lab: summer project map

summer reading map, otherwise these repos are going to blend together in my head. Main thing to keep asking: what's fixed input vs what the sampler can actually change?

• dated record: June 9 begins the 2025 summer lab meeting series. The meeting log records joining the series; it does not establish a first-ever lab visit or a completed technical result.

My phylogenetics notes: parsimony, homoplasy, and the Fitch algorithm.

• project navigation: the prior summer's TreeFam/PDB mapping work is in treefam-pdb-dataeng. The later evaluation work is in phylo-mcmc-evaluation. Use the latter for the Historian/BAli-Phy benchmark; keep the two projects' artifacts separate.

• reference questions for the summer: what is sampled jointly—tree, alignment, ancestral sequences and evolutionary parameters—and what is supplied as fixed input? Which outputs are scientific estimates versus debugging traces? The meeting entry is sparse, so these are review questions compiled for this reference notebook, not claimed quotations from the meeting.

• related reading path: June 23 pairHMM/substitution-model discussion; June 30 indel models and EvolDeeds; July brainstorming for joint-sample scoring and uncertainty visualization.