BAli-Phy: locating posterior artifacts

BAli-Phy wrote to baliphy-1, don't accidentally read the older folder. keep C1.run.json, numerical trace, trees + sampled alignments together; check the realized model there.

SCOPt3 log: output is written under data/simulation/SCOPt3e1/seq_1/baliphy-1/, despite the source file living in a folder named baliphy. The automatic suffix matters when pairing results with a run manifest.

Artifacts: C1.run.json records the run; C1.log is the numerical-parameter TSV; C1.trees contains sampled trees; C1.P<partition>.fastas contains sampled alignments. The recorded substitution setup is lg08 +> f(pi=lg08_freq) +> Rates.gamma(n=5, alpha=2.03507408419115), with rs07 rate about 0.423235 and mean length about 5.568688.

Runtime setting: maximum 2,200,000 iterations. The tool log explicitly leaves convergence monitoring to the user; a configured maximum is not evidence it ran to completion or converged.

Review question: ensure the parser reads the actual suffixed output directory, not a stale earlier run. Check the realized model and priors in C1.run.json rather than assuming a wrapper command's intended configuration was interpreted exactly as expected.

BAli-Phy DNA-trial summary: TN93, RS07, ACT, ESS, and burn-in.