Version 3.3.0

Highlights

• Improved selection criterion: Changed from omega_sum to omega_final (post-QC discordance)
• Robust tie-breaking: Multi-level tie-breaking ensures deterministic selection
• Better biological relevance: omega_final reflects true phylogenetic signal after QC
• Both modes updated: scRNA and spacetracer modes now use the same selection logic

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What's New

Algorithm Changes

• Primary criterion: omega_final (minimum) - selects the tree with best post-QC phylogenetic signal
• Tie-breaker 1: omega_sum (minimum) - resolves ties in omega_final
• Tie-breaker 2: omega_pre_qc (minimum) - resolves remaining ties
• Fallback: First candidate (deterministic)

Why This Matters

Previously, a tree with low omega_sum but high omega_final could be selected. Now, the tree with the best post-QC phylogenetic signal is prioritized, which is more biologically meaningful.

Output & Logging

• README now states: "Selection criterion: Minimum Omega (final)"
• Tie-breaking events are logged with candidate lists and selection rationale
• Final summary shows "selected by minimum Omega_final"

Backward Compatibility

• ✅ Fully backward compatible with v3.2.x
• ✅ No changes to input/output formats or command-line interfaces
• ⚠️ Selection behavior may change for some datasets - review final outputs

Files Changed

• src/run_phylosilid_fullTree_scRNA.py
• src/run_phylosilid_fullTree_spacetracer.py

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Notes

• Recommended for all users
• For detailed documentation: https://github.com/douyinlab/PhyloSOLID/