diff --git a/meteor/meteor.py b/meteor/meteor.py
index 7c3de95..69fae67 100644
--- a/meteor/meteor.py
+++ b/meteor/meteor.py
@@ -784,6 +784,7 @@ def main() -> None:  # pragma: no cover
             meteor,
             args.max_gap,
             args.min_info_sites,
+            args.gtr,
             args.width,
             args.height,
             args.format,
diff --git a/meteor/phylogeny.py b/meteor/phylogeny.py
index 534265d..618ce4f 100644
--- a/meteor/phylogeny.py
+++ b/meteor/phylogeny.py
@@ -63,7 +63,7 @@ def compute_site_info(self, sequences: Iterable[str]) -> list[float]:
 
     def clean_sites(
         self, msp_file: Path, output: tempfile._TemporaryFileWrapper
-    ) -> Tuple[dict[Union[int, str, None]], int]:
+    ) -> Tuple[dict[Union[int, str, None], str], int]:
         """Clean msp sequence according to a certain level of gap at each sites.
         :param msp_file: (Path) Fasta file
         :param output_file: (Path) Output cleaned fasta file