diff --git a/.gitignore b/.gitignore
index eeb5ed3..308676a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -68,3 +68,8 @@ ENV/
 
 # mypy
 .mypy_cache/
+
+# Test output files
+*.png
+*.pdf
+*.svg
diff --git a/src/flexidot/utils/alignments.py b/src/flexidot/utils/alignments.py
index c81f624..8454e63 100644
--- a/src/flexidot/utils/alignments.py
+++ b/src/flexidot/utils/alignments.py
@@ -133,7 +133,15 @@ def parse_blast6(
                 }
             )
 
-    logging.info(f'Parsed {len(alignments)} alignments from BLAST6 file: {filepath}')
+    if len(alignments) == 0:
+        logging.warning(
+            f'No alignments found in BLAST6 file: {filepath}. '
+            'Plot will be generated without alignment overlays.'
+        )
+    else:
+        logging.info(
+            f'Parsed {len(alignments)} alignments from BLAST6 file: {filepath}'
+        )
     return alignments
 
 
@@ -260,7 +268,13 @@ def parse_paf(
                 }
             )
 
-    logging.info(f'Parsed {len(alignments)} alignments from PAF file: {filepath}')
+    if len(alignments) == 0:
+        logging.warning(
+            f'No alignments found in PAF file: {filepath}. '
+            'Plot will be generated without alignment overlays.'
+        )
+    else:
+        logging.info(f'Parsed {len(alignments)} alignments from PAF file: {filepath}')
     return alignments
 
 
diff --git a/src/flexidot/utils/file_handling.py b/src/flexidot/utils/file_handling.py
index db0d373..04f1b2b 100644
--- a/src/flexidot/utils/file_handling.py
+++ b/src/flexidot/utils/file_handling.py
@@ -342,28 +342,33 @@ def read_gffs(
         )
         logging.info(text)
 
-    # create color legend
-    colors, alphas = [], []
-    for item in sorted(used_feats):
-        colors.append(color_dict[item][0])
-        alphas.append(color_dict[item][1])
-    legend_figure(
-        colors=colors,
-        lcs_shading_num=len(used_feats),
-        type_nuc=type_nuc,
-        bins=sorted(used_feats),
-        alphas=alphas,
-        gff_legend=True,
-        prefix=prefix,
-        filetype=filetype,
-    )
+    # check if any annotations were found
+    if len(used_feats) == 0:
+        text = 'Warning: No annotation records found in GFF file(s). Plot will be generated without annotations.\n'
+        logging.warning(text)
+    else:
+        # create color legend
+        colors, alphas = [], []
+        for item in sorted(used_feats):
+            colors.append(color_dict[item][0])
+            alphas.append(color_dict[item][1])
+        legend_figure(
+            colors=colors,
+            lcs_shading_num=len(used_feats),
+            type_nuc=type_nuc,
+            bins=sorted(used_feats),
+            alphas=alphas,
+            gff_legend=True,
+            prefix=prefix,
+            filetype=filetype,
+        )
 
-    # print settings
-    text = 'GFF Feature Types: %s\nGFF Colors:        %s' % (
-        ', '.join(sorted(used_feats)),
-        ', '.join(sorted(colors)),
-    )
-    logging.info(text)
+        # print settings
+        text = 'GFF Feature Types: %s\nGFF Colors:        %s' % (
+            ', '.join(sorted(used_feats)),
+            ', '.join(sorted(colors)),
+        )
+        logging.info(text)
 
     return feat_dict
 
@@ -548,6 +553,12 @@ def legend_figure(
         alphas = []
         alphas = [1] * len(colors)
 
+    # handle empty colors list
+    if len(colors) == 0:
+        text = 'Warning: No colors provided for legend. Skipping legend creation.\n'
+        logging.warning(text)
+        return None
+
     # legend data points
     data_points = list(range(len(colors)))
     if not gff_legend:
diff --git a/tests/test-data/empty.gff3 b/tests/test-data/empty.gff3
new file mode 100644
index 0000000..bbfaa17
--- /dev/null
+++ b/tests/test-data/empty.gff3
@@ -0,0 +1,2 @@
+##gff-version 3
+# This is an empty GFF3 file with only header and comments
diff --git a/tests/test_gff_handling.py b/tests/test_gff_handling.py
new file mode 100644
index 0000000..0275f8e
--- /dev/null
+++ b/tests/test_gff_handling.py
@@ -0,0 +1,104 @@
+"""Tests for GFF file handling functions."""
+
+from pathlib import Path
+
+from flexidot.utils.alignments import load_alignments
+from flexidot.utils.file_handling import read_gffs
+
+# Test data paths
+TEST_DATA_DIR = Path(__file__).parent / 'test-data'
+EMPTY_GFF_FILE = TEST_DATA_DIR / 'empty.gff3'
+EXAMPLE_GFF_FILE = TEST_DATA_DIR / 'example.gff3'
+
+
+class TestReadGffs:
+    """Tests for read_gffs function."""
+
+    def test_read_empty_gff(self):
+        """Test reading an empty GFF file with no annotation records."""
+        # Should not raise an error even with empty GFF
+        feat_dict = read_gffs(
+            str(EMPTY_GFF_FILE),
+            color_dict={'others': ('grey', 1, 0)},
+            type_nuc=True,
+            prefix='test',
+            filetype='png',
+        )
+        # Should return empty dictionary
+        assert feat_dict == {}
+
+    def test_read_valid_gff(self):
+        """Test reading a valid GFF file with annotations."""
+        feat_dict = read_gffs(
+            str(EXAMPLE_GFF_FILE),
+            color_dict={
+                'spacer1': ('blue', 1, 0),
+                'repeat_region': ('red', 1, 0),
+                'spacerzoom': ('green', 1, 0),
+                'spacer2': ('yellow', 1, 0),
+                'spacer3': ('purple', 1, 0),
+                'others': ('grey', 1, 0),
+            },
+            type_nuc=True,
+            prefix='test',
+            filetype='png',
+        )
+        # Should return non-empty dictionary
+        assert len(feat_dict) > 0
+        assert 'Seq2' in feat_dict
+
+    def test_read_multiple_gffs_with_empty(self):
+        """Test reading multiple GFF files where one is empty."""
+        feat_dict = read_gffs(
+            [str(EXAMPLE_GFF_FILE), str(EMPTY_GFF_FILE)],
+            color_dict={
+                'spacer1': ('blue', 1, 0),
+                'repeat_region': ('red', 1, 0),
+                'spacerzoom': ('green', 1, 0),
+                'spacer2': ('yellow', 1, 0),
+                'spacer3': ('purple', 1, 0),
+                'others': ('grey', 1, 0),
+            },
+            type_nuc=True,
+            prefix='test',
+            filetype='png',
+        )
+        # Should still work and return data from the non-empty file
+        assert len(feat_dict) > 0
+        assert 'Seq2' in feat_dict
+
+
+class TestEmptyAlignments:
+    """Tests for empty alignment file handling."""
+
+    def test_empty_blast6_file(self, tmp_path):
+        """Test reading an empty BLAST6 file."""
+        empty_file = tmp_path / 'empty.blast6'
+        empty_file.write_text('')
+
+        alignments = load_alignments(str(empty_file), file_format='blast6')
+        assert alignments == []
+
+    def test_empty_paf_file(self, tmp_path):
+        """Test reading an empty PAF file."""
+        empty_file = tmp_path / 'empty.paf'
+        empty_file.write_text('')
+
+        alignments = load_alignments(str(empty_file), file_format='paf')
+        assert alignments == []
+
+    def test_blast6_file_with_only_comments(self, tmp_path):
+        """Test reading a BLAST6 file with only comments."""
+        comment_file = tmp_path / 'comments.blast6'
+        comment_file.write_text('# This is a comment\n# Another comment\n')
+
+        alignments = load_alignments(str(comment_file), file_format='blast6')
+        assert alignments == []
+
+    def test_paf_file_with_only_comments(self, tmp_path):
+        """Test reading a PAF file with only comments."""
+        comment_file = tmp_path / 'comments.paf'
+        comment_file.write_text('# This is a comment\n# Another comment\n')
+
+        alignments = load_alignments(str(comment_file), file_format='paf')
+        assert alignments == []