EvolDeeds: uncertainty-display and data-cleaning notes

confidence coloring could be useful, but first: confidence in WHAT exactly. Same width doesn't mean same homology, and missing confidence needs its own color / legend.

uI idea: display confidence on alignment positions or tree nodes, rather than coloring every inferred structure as equally certain. The source identifies react-msaview as supporting MSA/tree display and customizable coloring, with additional implementation potentially needed for confidence views.

Equal alignment width with different homology pairs.

input cleaning issues from the shared brainstorm: singleton families, duplicate sequences, very short unaligned sequences, nonstandard amino-acid letters and mixed letter case. One contributor used a ten-amino-acid cutoff but explicitly called it project-dependent. Do not silently turn that exploratory threshold into a universal rule.

• review questions: what posterior statistic defines the displayed confidence? Is uncertainty in column homology comparable across samples with different alignment widths? Are tree-node identifiers stable under topology changes? Preserve a clear legend and distinguish missing/undefined confidence from low confidence.

• status: visualization proposal, not proof that confidence coloring was implemented. The precise day remains estimated from the working-document period.