PairHMM and substitution-model study pointers

substitutions vs indels vs alignment paths—separate piles before this becomes model soup. pairHMM: which paths get summed over, which one gets picked?

meeting topic: the June 23 log identifies substitution models of sequence evolution and pairwise-alignment models using pairHMMs. The dated log does not preserve the full lecture or equations.

reference concepts to keep separate: a substitution model describes residue changes; an alignment represents proposed homology; an indel model accounts for insertions/deletions; a tree supplies the evolutionary relationships/branch structure. Joint estimation makes uncertainty in one object relevant to the others.

My HMM notes: hidden states, transitions, and emissions.

My phylogenetics notes: distances, tree fitting, and Jukes–Cantor correction.

• related project reference: Historian, as linked in the evaluation proposal; paper. These are navigation links, not evidence that a specific software version was used in this meeting.

• review questions: what is conditioned on when computing a pairwise score? Which paths are summed over versus selected? How does changing an alignment affect the inferred ancestral state? Revisit the source presentation or study scan before reconstructing a detailed derivation; the summary log alone cannot supply one.