Kenneth ChengMathematical modeling

Editorial project overview

Phylogenetic Model Misspecification

Can more DNA increase confidence in the wrong topology when the inference model is structurally misspecified?

Reproducible studyUpdated 30 Jul 2026
Technical figure from Phylogenetic Model Misspecification
A reviewed research figure synchronized from the private technical workspace. The original aspect ratio and labels are preserved.

Editorial overview

Read When More DNA Makes the Wrong Tree More Certain for a full separation of sampling and model error, a composition-severity map, bootstrap interpretation, four approved figures, and a practical model-adequacy workflow.

Key findings

  • At 5000 sites under the heterogeneous generator, p-distance, JC69, and K80 recovered the true split in 0 of 120 alignments; regularized log-det recovered it in 120.
  • The selected alignment gave complete bootstrap support to incompatible splits under different distance models.

Limitations

  • The quartet and heterogeneous process are designed demonstrations.
  • The study does not establish that regularized log-det is universally superior.

Technical record

Detailed source, calculations, generated figures, and reproduction instructions are maintained in a private technical workspace. Public articles contain only manually reviewed interpretation and approved figures.

Version history

2026-07-30 — Curated overview reviewed against repository evidence.