Key takeaways:
✅ Use Count or GLOOME with maximum parsimony for accurate HGT inference;
⚠️ Gene trees introduce noise;
📌 If donor info is needed, use ALE with high stringency.

#HGT #genomics #evolution

Genes transferred together often remain neighbors, so we use genomic data to test real-world accuracy.
Fig. 2 is key:
🔺 Implicit methods (GLOOME, Count) vastly outperform others.
🔻 Explicit methods relying on gene trees show fewer co-transferred neighbors, suggesting higher false-positive rates.