Post-step: Phylogeny¶

This optional stage reconstructs lineage relationships from high-confidence mutation calls.

Input recommendation¶

Use curated loci after post-step recurrent-artifact filtering to reduce topology distortions from technical artifacts.

Input interpretation¶

Input	Interpretation
curated mutation loci (post-filtering)	Candidate mutation set used to build lineage relationships.
cell/spot mutation matrix	Presence/absence or probabilistic mutation matrix required by external phylogeny tools.

Parameter interpretation¶

Phylogeny parameters are backend-specific (for example tree model, bootstrap count, distance metric, mutation filtering stringency). Document these in your project phylogeny script to keep lineage results reproducible.

Tooling¶

SpaceTracer does not enforce a single phylogeny backend. You can integrate external tools (for example project-standard SNV phylogeny packages) using SpaceTracer outputs as input.

Suggested practice¶

• keep one reproducible export of loci/cell matrices used for tree building
• validate stability across filtering/stringency settings
• cross-check tree structure with tissue spatial context