nscorley · Oct 5, 2026 · Oct 5, 2026
diff --git a/docs/conf.py b/docs/conf.py
@@ -27,6 +27,7 @@
     "sphinx.ext.viewcode",  # Add source code links
     "sphinx.ext.napoleon",  # Google/NumPy style docstrings
     "sphinx_gallery.gen_gallery",  # Generates auto_examples/ from examples/
+    "sphinxcontrib.typer",
     "myst_parser",  # Support Markdown tutorial pages
     "sphinx_design",  # Render collapsible tutorial code examples
 ]
@@ -35,7 +36,7 @@
 html_favicon = "_static/favicon-32x32.png"
 
 templates_path = ["_templates"]
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "examples/GALLERY_HEADER.rst", "ml/preprocessing.rst"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "examples/GALLERY_HEADER.rst"]
 napoleon_use_ivar = True
 
 # -- Options for HTML output -------------------------------------------------

diff --git a/docs/docs_requirements.txt b/docs/docs_requirements.txt
@@ -8,3 +8,4 @@ ghp-import>=2.0.0,<3
 pandoc>=2.0.0,<3
 myst-parser>=5.0.0
 sphinx-design>=0.6.0,<1
+sphinxcontrib-typer>=0.7.2,<1
diff --git a/docs/index.rst b/docs/index.rst
@@ -27,3 +27,4 @@ Welcome to **atomworks** — a toolkit for converting, parsing, and manipulating
    auto_examples/index
    contributor_guide
    mirrors
+   msa
diff --git a/docs/ml.rst b/docs/ml.rst
@@ -25,3 +25,4 @@ Data Processing Modules
    ml/msa_server
    ml/transforms/msa
    ml/utils
+   ml/preprocessing
diff --git a/docs/ml/preprocessing.rst b/docs/ml/preprocessing.rst
@@ -6,7 +6,7 @@ This module contains utilities for preprocessing molecular structures and data.
 Core Preprocessing Functions
 ----------------------------
 
-.. automodule:: atomworks.ml.preprocessing.get_pn_unit_data_from_structure
+.. automodule:: atomworks.ml.preprocessing.preprocess
    :members:
    :undoc-members:
    :show-inheritance:
@@ -25,4 +25,43 @@ Utilities
 .. automodule:: atomworks.ml.preprocessing.utils
    :members:
    :undoc-members:
-   :show-inheritance: 
+   :show-inheritance:
+
+
+MSA
+---
+
+Note that the following functions can be called via the command line. See :doc:`../msa`
+for more details.
+
+Finding
+^^^^^^^
+
+.. automodule:: atomworks.ml.preprocessing.msa.finding
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Filtering
+^^^^^^^^^
+
+.. automodule:: atomworks.ml.preprocessing.msa.filtering
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Generating
+^^^^^^^^^^
+
+.. automodule:: atomworks.ml.preprocessing.msa.generating
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Organizing
+^^^^^^^^^^
+
+.. automodule:: atomworks.ml.preprocessing.msa.organizing
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/msa.rst b/docs/msa.rst
@@ -0,0 +1,38 @@
+Multiple Sequence Alignment in AtomWorks
+========================================
+
+AtomWorks provides several command-line tools for Multiple Sequence Alignment (MSA) operations.
+
+Install AtomWorks with the ML extra. Filtering requires hhfilter from HH-suite
+on PATH. Local generation requires the selected MMseqs2 or HHblits backend and
+configured sequence databases, plus hhfilter for filtering the results. The
+ColabFold Python API supports remote generation; see :doc:`ml/msa_server`.
+Finding and organizing existing files do not run a sequence search.
+
+Find
+----
+
+Provide ``--existing-msa-dirs`` or set ``PROTEIN_MSA_DIRS`` to the directories
+containing your MSA files.
+
+.. typer:: atomworks_cli.find:app
+    :prog: atomworks msa find
+    :show-nested:
+
+Filter
+------
+.. typer:: atomworks_cli.filter:app
+    :prog: atomworks msa filter
+    :show-nested:
+
+Generate
+--------
+.. typer:: atomworks_cli.generate:app
+    :prog: atomworks msa generate
+    :show-nested:
+
+Organize
+--------
+.. typer:: atomworks_cli.organize:app
+    :prog: atomworks msa organize
+    :show-nested:
diff --git a/pyproject.toml b/pyproject.toml
@@ -111,6 +111,7 @@ dev = [
 ]
 
 docs = [
+    "sphinxcontrib-typer>=0.7.2,<1",
     "sphinx>=8.0.0",
     "sphinx-gallery>=0.19.0",
     "pydata-sphinx-theme>=0.16.1",

diff --git a/src/atomworks/ml/preprocessing/msa/finding.py b/src/atomworks/ml/preprocessing/msa/finding.py
@@ -350,6 +350,7 @@ def find_template_alignments(
     Args:
         sequences: Protein sequences to find template alignments for.
         template_dirs: Directories to search. Accepts:
+
             - None: No directories (all sequences reported missing).
             - list[PathLike]: Auto-assumes ``.m8`` / directory_depth=2 (matching
               `organize_template_alignments`'s defaults).
-Original file line number
+Diff line change
@@ Expand Up @@
        auto_examples/index
        contributor_guide
        mirrors
+       msa