Inspecting spurious convergence using csubst site

Inspecting spurious convergence using csubst sites

This page keeps the historical URL, but the current command is csubst sites (csubst site remains a legacy alias).

Typical spurious-convergence cases can be examined through the summary PDF written by csubst sites:

• csubst_sites.pdf
• csubst_sites.<PDB_ID>.pdf when --pdb is used

For a general guide to current csubst sites outputs, see: Interpreting output files of csubst sites

Reliable pattern

Spurious case 1: Unnaturally localized convergent/divergent substitutions

This pattern often appears in misaligned sequences, including cases where splicing variants are represented inconsistently among species. In these examples, the near-complete absence of synonymous convergence (the gray bars in the summary PDF) makes it difficult for even ω_C to suppress the false signal completely.

For background, see Supplementary Text 12 in Fukushima & Pollock (2023).