.

Author: vsc20958

recmpox/recmpox.py

@@ -1684,6 +1684,8 @@ def _sample_key_from_tract(hid: str, label: str) -> str:
         cmd_iqtree = [
             "iqtree",
             "-s", str(aln_in_phylogeny),
+            # Always use the default GTR substitution model; do not run model selection.
+            "-m", "GTR",
             "-bb", "10000",
             "-pre", str(iqtree_prefix),
             "-czb",