diff --git a/bactria/__init__py.py b/bactria/__init__py.py
new file mode 100644
index 0000000..e69de29
diff --git a/bactria/tools/__init__.py b/bactria/tools/__init__.py
new file mode 100644
index 0000000..6eaec50
--- /dev/null
+++ b/bactria/tools/__init__.py
@@ -0,0 +1,19 @@
+from .blastdb_aliastool import BlastdbAliastool
+from .blastdbcmd import Blastdbcmd
+from .blastn import Blastn
+from .hmmalign import Hmmalign
+from .makeblastdb import Makeblastdb
+from .megatree_loader import MegatreeLoader
+from .megatree_pruner import MegatreePruner
+from .raxml_ng import RaxmlNg
+
+__all__ = [
+    'BlastdbAliastool',
+    'Blastdbcmd',
+    'Blastn',
+    'Hmmalign',
+    'Makeblastdb',
+    'MegatreeLoader',
+    'MegatreePruner',
+    'RaxmlNg',
+]
\ No newline at end of file
diff --git a/bactria/blastdb_aliastool.py b/bactria/tools/blastdb_aliastool.py
similarity index 99%
rename from bactria/blastdb_aliastool.py
rename to bactria/tools/blastdb_aliastool.py
index 9c64b19..6ac053f 100644
--- a/bactria/blastdb_aliastool.py
+++ b/bactria/tools/blastdb_aliastool.py
@@ -1,5 +1,5 @@
 from typing import Optional, List
-from bactria.tool_runner import ToolRunner
+from .tool_runner import ToolRunner
 from bactria.config import Config
 
 
diff --git a/bactria/blastdbcmd.py b/bactria/tools/blastdbcmd.py
similarity index 98%
rename from bactria/blastdbcmd.py
rename to bactria/tools/blastdbcmd.py
index 2ba39af..5892aa2 100644
--- a/bactria/blastdbcmd.py
+++ b/bactria/tools/blastdbcmd.py
@@ -1,16 +1,16 @@
 from typing import Optional, List
-from bactria.tool_runner import ToolRunner
+from .tool_runner import ToolRunner
 from bactria.config import Config
 
 
-class Blastdbcommand(ToolRunner):
+class Blastdbcmd(ToolRunner):
     """
     A subclass of ToolRunner specifically for running blastdbcmd.
 
     Examples:
         >>> config = Config()
         >>> config.load_config('path/to/config.yaml')
-        >>> blastdbcmd_runner = Blastdbcommand(config)
+        >>> blastdbcmd_runner = Blastdbcmd(config)
         >>> blastdbcmd_runner.set_db('nr')
         >>> blastdbcmd_runner.set_entry(['NP_000508.1', 'NP_001018081.2'])
         >>> blastdbcmd_runner.set_outfmt('%f')
diff --git a/bactria/blastn.py b/bactria/tools/blastn.py
similarity index 98%
rename from bactria/blastn.py
rename to bactria/tools/blastn.py
index b9165bd..b81b26a 100644
--- a/bactria/blastn.py
+++ b/bactria/tools/blastn.py
@@ -1,16 +1,16 @@
 from typing import List, Union
-from bactria.tool_runner import ToolRunner
+from .tool_runner import ToolRunner
 from bactria.config import Config
 
 
-class BLASTN(ToolRunner):
+class Blastn(ToolRunner):
     """
     A subclass of ToolRunner specifically for running BLASTN (Nucleotide-Nucleotide BLAST).
 
     Examples:
         >>> config = Config()
         >>> config.load_config('path/to/config.yaml')
-        >>> blastn_runner = BLASTN(config)
+        >>> blastn_runner = Blastn(config)
         >>> blastn_runner.set_query('input.fasta')
         >>> blastn_runner.set_db('nr')
         >>> blastn_runner.set_out('output.txt')
diff --git a/bactria/hmmalign.py b/bactria/tools/hmmalign.py
similarity index 99%
rename from bactria/hmmalign.py
rename to bactria/tools/hmmalign.py
index 01e2ad9..abd0aa8 100644
--- a/bactria/hmmalign.py
+++ b/bactria/tools/hmmalign.py
@@ -1,5 +1,5 @@
 from typing import List
-from bactria.tool_runner import ToolRunner
+from .tool_runner import ToolRunner
 from bactria.config import Config
 
 
diff --git a/bactria/makeblastdb.py b/bactria/tools/makeblastdb.py
similarity index 100%
rename from bactria/makeblastdb.py
rename to bactria/tools/makeblastdb.py
diff --git a/bactria/megatree_loader.py b/bactria/tools/megatree_loader.py
similarity index 100%
rename from bactria/megatree_loader.py
rename to bactria/tools/megatree_loader.py
diff --git a/bactria/megatree_pruner.py b/bactria/tools/megatree_pruner.py
similarity index 100%
rename from bactria/megatree_pruner.py
rename to bactria/tools/megatree_pruner.py
diff --git a/bactria/raxml_ng.py b/bactria/tools/raxml_ng.py
similarity index 98%
rename from bactria/raxml_ng.py
rename to bactria/tools/raxml_ng.py
index 8a45444..22d6d3b 100644
--- a/bactria/raxml_ng.py
+++ b/bactria/tools/raxml_ng.py
@@ -1,16 +1,16 @@
 from typing import Optional, List, Union
-from bactria.tool_runner import ToolRunner
+from .tool_runner import ToolRunner
 from bactria.config import Config
 
 
-class RAXMLNG(ToolRunner):
+class RaxmlNg(ToolRunner):
     """
     A subclass of ToolRunner specifically for running RAxML-NG (Randomized Axelerated Maximum Likelihood - Next Generation).
 
     Examples:
         >>> config = Config()
         >>> config.load_config('path/to/config.yaml')
-        >>> raxml_runner = RAXMLNG(config)
+        >>> raxml_runner = RaxmlNg(config)
         >>> raxml_runner.set_msa('alignment.fa')
         >>> raxml_runner.set_model('GTR+G')
         >>> raxml_runner.set_prefix('test_run')
diff --git a/bactria/tool_runner.py b/bactria/tools/tool_runner.py
similarity index 100%
rename from bactria/tool_runner.py
rename to bactria/tools/tool_runner.py