diff --git a/biology/py-biopython/Makefile b/biology/py-biopython/Makefile
index d735696d98b..e36f4f4e1e4 100644
--- a/biology/py-biopython/Makefile
+++ b/biology/py-biopython/Makefile
@@ -1,14 +1,16 @@
-# $OpenBSD: Makefile,v 1.11 2008/01/11 09:28:20 winiger Exp $
+# $OpenBSD: Makefile,v 1.12 2008/01/12 02:00:24 okan Exp $
 
 SHARED_ONLY=	Yes
 COMMENT=	Python tools for computational molecular biology
 
-DISTNAME=	biopython-1.41
-PKGNAME=	py-${DISTNAME}p4
+DISTNAME=	biopython-1.44
+PKGNAME=	py-${DISTNAME}
 CATEGORIES=	biology
 
 HOMEPAGE=	http://www.biopython.org/
 
+MAINTAINER=	Will Maier <willmaier@ml1.net>
+
 # BSD-like 
 PERMIT_PACKAGE_CDROM=	Yes
 PERMIT_PACKAGE_FTP=	Yes
@@ -20,26 +22,28 @@ MASTER_SITES=	${HOMEPAGE}DIST/
 MODULES=	lang/python
 PY_FLAVOR=	python${MODPY_VERSION}
 
+WANTLIB+=	stdc++
+
 BUILD_DEPENDS=	${MODPY_EXPAT_DEPENDS} \
-		::math/py-Numeric 
+		::math/py-Numeric \
+		::devel/swig
 RUN_DEPENDS=	${MODPY_EXPAT_DEPENDS} \
 		:py-mxDateTime-*-${PY_FLAVOR}:devel/py-mxDateTime,${PY_FLAVOR} \
 		:py-Numeric-*:math/py-Numeric \
 		:py-reportlab-*:print/py-reportlab/reportlab
 REGRESS_DEPENDS=${RUN_DEPENDS}
 
-EXAMPLESDIR=	${PREFIX}/share/examples/py-biopython
-
-pre-configure:
-	@echo '5\nm2\nwq' | ed -s ${WRKSRC}/Bio/Wise/dnal.py
+CFLAGS+=	-fPIC
 
 post-install:
-	${INSTALL_DATA_DIR} ${EXAMPLESDIR}
-	cd ${WRKSRC}/Tests; tar cf - * | tar xf - -C ${EXAMPLESDIR} 
+	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/py-biopython/
+	${INSTALL_DATA_DIR} ${PREFIX}/share/examples/py-biopython/
+	${INSTALL_DATA} ${WRKSRC}/Doc/*.txt ${PREFIX}/share/doc/py-biopython/
+	cd ${WRKSRC}/Doc/examples; tar cf - * | \
+		tar xf - -C ${PREFIX}/share/examples/py-biopython
 
 do-regress: fake
-	@rm -f ${WRKSRC}/Tests/test_copen.py*
-	@cd ${WRKSRC}/Tests && ${MAKE_ENV} \
+	@cd ${WRKSRC}/Tests && \
 		PYTHONPATH=${WRKINST}${MODPY_SITEPKG} \
 		${MODPY_BIN} ./run_tests.py --no-gui
 
diff --git a/biology/py-biopython/distinfo b/biology/py-biopython/distinfo
index 99c41ef83a4..0a673915b28 100644
--- a/biology/py-biopython/distinfo
+++ b/biology/py-biopython/distinfo
@@ -1,5 +1,5 @@
-MD5 (biopython-1.41.tar.gz) = A/jvwlj7SbB9GitkL6g2Lg==
-RMD160 (biopython-1.41.tar.gz) = 961eFwpqN0D6vjgocVuD/Ew+Fa4=
-SHA1 (biopython-1.41.tar.gz) = p6O6xgasxbW3ClZUAvnCgSCbqLk=
-SHA256 (biopython-1.41.tar.gz) = FbcIt2Nf2ZOq08U/1M/ChgHabUMysCfQmJnxy1F4zvk=
-SIZE (biopython-1.41.tar.gz) = 3807547
+MD5 (biopython-1.44.tar.gz) = dix6NYr53Fi3Eri0u5nQwg==
+RMD160 (biopython-1.44.tar.gz) = 7Lvi9G8OXRJNkQYy3Jp/0FEgLAs=
+SHA1 (biopython-1.44.tar.gz) = yio1yekqIZJW/k/CojLfUyj59dk=
+SHA256 (biopython-1.44.tar.gz) = 5HxKfGEuEctsHAUVJ0ziMWRrMbvxyeOsWJmJKMCtPHI=
+SIZE (biopython-1.44.tar.gz) = 3840036
diff --git a/biology/py-biopython/patches/patch-Bio_Cluster_clustermodule_c b/biology/py-biopython/patches/patch-Bio_Cluster_clustermodule_c
deleted file mode 100644
index dc001e077d0..00000000000
--- a/biology/py-biopython/patches/patch-Bio_Cluster_clustermodule_c
+++ /dev/null
@@ -1,216 +0,0 @@
-$OpenBSD: patch-Bio_Cluster_clustermodule_c,v 1.2 2007/10/18 15:22:15 ajacoutot Exp $
---- Bio/Cluster/clustermodule.c.orig	Wed Apr 27 10:09:08 2005
-+++ Bio/Cluster/clustermodule.c	Thu Oct 18 17:11:50 2007
-@@ -111,7 +111,7 @@ parse_mask (PyObject* object, PyArrayObject** array, c
-     return mask;
-   }
-   if(!PyArray_Check (object)) /* Try to convert object to a 2D double array */
--  { *array = (PyArrayObject*) PyArray_FromObject(object, PyArray_LONG, 2, 2);
-+  { *array = (PyArrayObject*) PyArray_FromObject(object, PyArray_INT, 2, 2);
-     if (!(*array))
-     { strcpy (message, "mask cannot be converted to needed array");
-       PyErr_SetString(ErrorObject, buffer);
-@@ -121,8 +121,8 @@ parse_mask (PyObject* object, PyArrayObject** array, c
-   else /* User passed an array */
-   { *array = (PyArrayObject*) object;
-     Py_INCREF(object);
--    if ((*array)->descr->type_num != PyArray_LONG)
--    { PyArrayObject* av = (PyArrayObject*) PyArray_Cast (*array, PyArray_LONG);
-+    if ((*array)->descr->type_num != PyArray_INT)
-+    { PyArrayObject* av = (PyArrayObject*) PyArray_Cast (*array, PyArray_INT);
-       Py_DECREF((PyObject*) *array);
-       *array = av;
-       if (!(*array))
-@@ -281,7 +281,7 @@ parse_initialid(PyObject* object, int* nclusters, int 
-   PyArrayObject* array;
-   /* -- First we create the clusterid variable ------------------------ */
-   PyArrayObject* clusterid =
--    (PyArrayObject*) PyArray_FromDims(1, &nitems, PyArray_LONG);
-+    (PyArrayObject*) PyArray_FromDims(1, &nitems, PyArray_INT);
-   if (!clusterid)
-   { strcpy(message, "Could not create clusterid array -- too big?");
-     PyErr_SetString (ErrorObject, buffer);
-@@ -291,7 +291,7 @@ parse_initialid(PyObject* object, int* nclusters, int 
-   if (object==NULL) return clusterid;
-   /* -- Check if the specified object is an array --------------------- */
-   if(!PyArray_Check (object))
--  { array = (PyArrayObject*) PyArray_FromObject(object, PyArray_LONG,1,1);
-+  { array = (PyArrayObject*) PyArray_FromObject(object, PyArray_INT,1,1);
-     if (!array)
-     { strcpy (message, "initialid cannot be converted to needed array.");
-       PyErr_SetString(ErrorObject, buffer);
-@@ -304,8 +304,8 @@ parse_initialid(PyObject* object, int* nclusters, int 
-     Py_INCREF(object);
-   }
-   /* -- Check if the array contains integers -------------------------- */
--  if (array->descr->type_num != PyArray_LONG)
--  { PyArrayObject* av = (PyArrayObject*) PyArray_Cast(array, PyArray_LONG);
-+  if (array->descr->type_num != PyArray_INT)
-+  { PyArrayObject* av = (PyArrayObject*) PyArray_Cast(array, PyArray_INT);
-     Py_DECREF((PyObject*) array);
-     array = av;
-     if (!array)
-@@ -394,7 +394,7 @@ parse_clusterid(PyObject* object, PyArrayObject** arra
-   }
-   /* -- The user specified something. Let's see if it is an array ----- */
-   if(!PyArray_Check (object))
--  { *array = (PyArrayObject*) PyArray_FromObject(object, PyArray_LONG,1,1);
-+  { *array = (PyArrayObject*) PyArray_FromObject(object, PyArray_INT,1,1);
-     if (!(*array))
-     { strcpy (message, "clusterid cannot be converted to needed array.");
-       PyErr_SetString(ErrorObject, buffer);
-@@ -406,8 +406,8 @@ parse_clusterid(PyObject* object, PyArrayObject** arra
-     Py_INCREF(object);
-   }
-   /* -- Check if the array contains integers -------------------------- */
--  if ((*array)->descr->type_num != PyArray_LONG)
--  { PyArrayObject* av = (PyArrayObject*) PyArray_Cast(*array, PyArray_LONG);
-+  if ((*array)->descr->type_num != PyArray_INT)
-+  { PyArrayObject* av = (PyArrayObject*) PyArray_Cast(*array, PyArray_INT);
-     Py_DECREF((PyObject*) (*array));
-     *array = av;
-     if (!(*array))
-@@ -663,7 +663,7 @@ parse_index(PyObject* object, PyArrayObject** array, i
-   /* Check if the user specified an array */
-   if(!PyArray_Check (object)) /* Try to convert to an array of type long */
-   { *array = (PyArrayObject*)
--      PyArray_ContiguousFromObject(object, PyArray_LONG, 1, 1);
-+      PyArray_ContiguousFromObject(object, PyArray_INT, 1, 1);
-     if (!(*array))
-     { strcpy(message, "index argument cannot be converted to needed type.");
-       PyErr_SetString (ErrorObject, buffer);
-@@ -672,7 +672,7 @@ parse_index(PyObject* object, PyArrayObject** array, i
-     }
-   }
-   /* If an array, make sure it contains integers */
--  else if ((*array)->descr->type_num == PyArray_LONG)
-+  else if ((*array)->descr->type_num == PyArray_INT)
-   { *array = (PyArrayObject*) object;
-     Py_INCREF(object);
-   }
-@@ -697,7 +697,7 @@ parse_index(PyObject* object, PyArrayObject** array, i
-   }
-   if (!(*array)->flags & CONTIGUOUS)
-   { PyObject* av =
--      PyArray_ContiguousFromObject((PyObject*) array, PyArray_LONG, 0, 0);
-+      PyArray_ContiguousFromObject((PyObject*) array, PyArray_INT, 0, 0);
-     Py_DECREF(object); /* can only happen if *array==(PyArrayObject*)object */
-     if(!av)
-     { strcpy(message, "Failed making argument index contiguous.");
-@@ -800,7 +800,7 @@ py_kcluster (PyObject* self, PyObject* args, PyObject*
-                             "dist",
-                             "initialid",
-                              NULL };
--  if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|lOOllccO", kwlist,
-+  if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|iOOiiccO", kwlist,
-                                   &DATA,
-                                   &NCLUSTERS,
-                                   &MASK,
-@@ -899,7 +899,7 @@ py_kcluster (PyObject* self, PyObject* args, PyObject*
-   free_weight(aWEIGHT, weight);
-   /* --------------------------------------------------------------------- */
- 
--  return Py_BuildValue("Ndl", aCLUSTERID, ERROR, IFOUND);
-+  return Py_BuildValue("Ndi", aCLUSTERID, ERROR, IFOUND);
- } 
- /* end of wrapper for kcluster */
- 
-@@ -1015,7 +1015,7 @@ py_kmedoids (PyObject* self, PyObject* args, PyObject*
-     strcpy(message, "Unknown error in kmedoids");
-     return NULL;
-   }
--  return Py_BuildValue("Ndl",aCLUSTERID, ERROR, IFOUND);
-+  return Py_BuildValue("Ndi",aCLUSTERID, ERROR, IFOUND);
- } 
- /* end of wrapper for kmedoids */
- 
-@@ -1091,7 +1091,7 @@ py_treecluster (PyObject* self, PyObject* args, PyObje
-                             "dist",
-                             "distancematrix",
-                              NULL };
--  if(!PyArg_ParseTupleAndKeywords(args, keywords, "|OOOlccO", kwlist,
-+  if(!PyArg_ParseTupleAndKeywords(args, keywords, "|OOOiccO", kwlist,
-                                   &DATA,
-                                   &MASK,
-                                   &WEIGHT,
-@@ -1165,7 +1165,7 @@ py_treecluster (PyObject* self, PyObject* args, PyObje
-     /* -- Create the output variable tree ---------------------------------- */
-     shape[0] = nnodes;
-     shape[1] = 2;
--    aRESULT = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_LONG);
-+    aRESULT = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_INT);
-     if (!aRESULT)
-     { strcpy(message, "Could not create array for return value -- too big?");
-       PyErr_SetString(ErrorObject, buffer);
-@@ -1228,7 +1228,7 @@ py_treecluster (PyObject* self, PyObject* args, PyObje
-     /* -- Create the output variable tree ---------------------------------- */
-     shape[0] = nnodes;
-     shape[1] = 2;
--    aRESULT = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_LONG);
-+    aRESULT = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_INT);
-     if (!aRESULT)
-     { strcpy(message, "Could not create array for return value -- too big?");
-       PyErr_SetString(ErrorObject, buffer);
-@@ -1341,7 +1341,7 @@ py_somcluster (PyObject* self, PyObject* args, PyObjec
-                             "niter",
-                             "dist",
-                              NULL };
--  if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|OOllldlc", kwlist,
-+  if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|OOiiidic", kwlist,
-                                   &DATA,
-                                   &MASK,
-                                   &WEIGHT,
-@@ -1403,7 +1403,7 @@ py_somcluster (PyObject* self, PyObject* args, PyObjec
-   /* --------------------------------------------------------------------- */
-   shape[0] = nitems;
-   shape[1] = 2;
--  aCLUSTERID = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_LONG);
-+  aCLUSTERID = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_INT);
-   if (!aCLUSTERID)
-   { strcpy(buffer, "somcluster: Could not create clusterid array -- too big?");
-     PyErr_SetString (ErrorObject, buffer);
-@@ -1656,7 +1656,7 @@ py_clusterdistance (PyObject* self, PyObject* args, Py
-                             "dist",
-                             "transpose",
-                              NULL };
--  if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|OOOOccl", kwlist,
-+  if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|OOOOcci", kwlist,
-                                   &DATA,
-                                   &MASK,
-                                   &WEIGHT,
-@@ -1826,7 +1826,7 @@ py_clustercentroid (PyObject* self, PyObject* args, Py
-   for (i=0; i<shape[0]; i++)
-     cdata[i] = ((double*) (aCDATA->data)) + i*shape[1];
-   /* -- Create the centroid mask output variable ------------------------- */
--  aCMASK = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_LONG);
-+  aCMASK = (PyArrayObject*) PyArray_FromDims(2, shape, PyArray_INT);
-   if (!aCMASK)
-   { strcpy(message, "Could not create centroids array -- too big?");
-     PyErr_SetString (ErrorObject, buffer);
-@@ -1934,7 +1934,7 @@ py_distancematrix (PyObject* self, PyObject* args, PyO
-                             "transpose",
-                             "dist",
-                              NULL };
--  if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|OOlc", kwlist,
-+  if(!PyArg_ParseTupleAndKeywords(args, keywords, "O|OOic", kwlist,
-                                   &DATA,
-                                   &MASK,
-                                   &WEIGHT,
-@@ -2056,7 +2056,7 @@ py_cuttree (PyObject* self, PyObject* args, PyObject* 
-   { aTREE = (PyArrayObject*) TREE;
-     Py_INCREF((PyObject*) aTREE);
-   }
--  if (aTREE->descr->type_num != PyArray_LONG)
-+  if (aTREE->descr->type_num != PyArray_INT)
-   { PyErr_SetString (ErrorObject,
-       "cuttree: Argument tree should contain integer values only");
-     return NULL;
-@@ -2095,7 +2095,7 @@ py_cuttree (PyObject* self, PyObject* args, PyObject* 
-     return NULL;
-   }
-   /* -- Create the clusterid output variable ----------------------------- */
--  aCLUSTERID = (PyArrayObject*) PyArray_FromDims(1, &NELEMENTS, PyArray_LONG);
-+  aCLUSTERID = (PyArrayObject*) PyArray_FromDims(1, &NELEMENTS, PyArray_INT);
-   if (!aCLUSTERID) {
-     PyErr_SetString (ErrorObject,
-       "cuttree: Could not create array for return value -- too big?");
diff --git a/biology/py-biopython/patches/patch-Tests_run_tests_py b/biology/py-biopython/patches/patch-Tests_run_tests_py
index d1655219056..febe114db0f 100644
--- a/biology/py-biopython/patches/patch-Tests_run_tests_py
+++ b/biology/py-biopython/patches/patch-Tests_run_tests_py
@@ -1,7 +1,7 @@
-$OpenBSD: patch-Tests_run_tests_py,v 1.1 2005/12/03 22:34:52 alek Exp $
---- Tests/run_tests.py.orig	Sun Nov 20 16:29:24 2005
-+++ Tests/run_tests.py	Sun Nov 20 16:29:35 2005
-@@ -37,11 +37,11 @@ def main(argv):
+$OpenBSD: patch-Tests_run_tests_py,v 1.2 2008/01/12 02:00:24 okan Exp $
+--- Tests/run_tests.py.orig	Thu Oct 11 20:39:07 2007
++++ Tests/run_tests.py	Fri Dec 21 16:45:24 2007
+@@ -39,11 +39,11 @@ def main(argv):
      # A. Because Martel may not be in ../build/lib.*
      test_path = sys.path[0] or "."
      source_path = os.path.abspath("%s/.." % test_path)
diff --git a/biology/py-biopython/patches/patch-setup_py b/biology/py-biopython/patches/patch-setup_py
index 6cb7040a067..87465ee6857 100644
--- a/biology/py-biopython/patches/patch-setup_py
+++ b/biology/py-biopython/patches/patch-setup_py
@@ -1,15 +1,22 @@
-$OpenBSD: patch-setup_py,v 1.4 2005/12/18 20:33:17 alek Exp $
---- setup.py.orig	Fri Oct 28 21:41:02 2005
-+++ setup.py	Sun Dec 18 19:26:31 2005
-@@ -65,6 +65,7 @@ def check_dependencies_once():
+$OpenBSD: patch-setup_py,v 1.5 2008/01/12 02:00:24 okan Exp $
+--- setup.py.orig	Sat Oct 27 02:11:01 2007
++++ setup.py	Fri Dec 21 16:56:57 2007
+@@ -65,6 +65,14 @@ def check_dependencies_once():
      return _CHECKED
  
  def check_dependencies():
++    NUMPY_PACKAGES.append("Bio.KDTree")
++    NUMPY_EXTENSIONS.append(
++        CplusplusExtension('Bio.KDTree._CKDTree', 
++                           ["Bio/KDTree/KDTree.cpp",
++                            "Bio/KDTree/KDTree.swig.cpp"],
++                           libraries=["stdc++"],
++                           language="c++"))
 +    return 1
      """Return whether the installation should continue."""
      # There should be some way for the user to tell specify not to
      # check dependencies.  For example, it probably should not if
-@@ -254,7 +255,10 @@ def is_Martel_installed():
+@@ -285,7 +293,10 @@ def is_Martel_installed():
          bundled_martel_version = m.__version__
      else:
          bundled_martel_version = None
diff --git a/biology/py-biopython/pkg/PFRAG.shared b/biology/py-biopython/pkg/PFRAG.shared
new file mode 100644
index 00000000000..668cf2d985c
--- /dev/null
+++ b/biology/py-biopython/pkg/PFRAG.shared
@@ -0,0 +1,2 @@
+@comment $OpenBSD: PFRAG.shared,v 1.1 2008/01/12 02:00:24 okan Exp $
+lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/_CKDTree.so
diff --git a/biology/py-biopython/pkg/PLIST b/biology/py-biopython/pkg/PLIST
index 31af2292f7d..05e24fed37e 100644
--- a/biology/py-biopython/pkg/PLIST
+++ b/biology/py-biopython/pkg/PLIST
@@ -1,4 +1,5 @@
-@comment $OpenBSD: PLIST,v 1.5 2007/11/02 10:10:11 ajacoutot Exp $
+@comment $OpenBSD: PLIST,v 1.6 2008/01/12 02:00:24 okan Exp $
+%%SHARED%%
 lib/python${MODPY_VERSION}/site-packages/Bio/
 lib/python${MODPY_VERSION}/site-packages/Bio/Affy/
 lib/python${MODPY_VERSION}/site-packages/Bio/Affy/CelFile.py
@@ -8,8 +9,6 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Affy/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Ais/
 lib/python${MODPY_VERSION}/site-packages/Bio/Ais/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Ais/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Ais/example_ais2.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Ais/example_ais2.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Align/
 lib/python${MODPY_VERSION}/site-packages/Bio/Align/AlignInfo.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Align/AlignInfo.pyc
@@ -78,8 +77,6 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Cluster/
 lib/python${MODPY_VERSION}/site-packages/Bio/Cluster/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Cluster/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Cluster/cluster.so
-lib/python${MODPY_VERSION}/site-packages/Bio/Cluster/data.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Cluster/data.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Compass/
 lib/python${MODPY_VERSION}/site-packages/Bio/Compass/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Compass/__init__.pyc
@@ -252,6 +249,8 @@ lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/LocationParser.py
 lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/LocationParser.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/Record.py
 lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/Record.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/Scanner.py
+lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/Scanner.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/utils.py
@@ -261,8 +260,6 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Geo/Record.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Geo/Record.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Geo/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Geo/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Geo/geo_format.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Geo/geo_format.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Gobase/
 lib/python${MODPY_VERSION}/site-packages/Bio/Gobase/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Gobase/__init__.pyc
@@ -302,31 +299,25 @@ lib/python${MODPY_VERSION}/site-packages/Bio/IntelliGenetics/intelligenetics_for
 lib/python${MODPY_VERSION}/site-packages/Bio/InterPro/
 lib/python${MODPY_VERSION}/site-packages/Bio/InterPro/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/InterPro/__init__.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/
+lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/CKDTree.py
+lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/CKDTree.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/KDTree.py
+lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/KDTree.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/__init__.py
+lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/
 lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Compound/
 lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Compound/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Compound/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Compound/compound_format.py
-lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Compound/compound_format.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Enzyme/
 lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Enzyme/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Enzyme/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Enzyme/enzyme_format.py
-lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Enzyme/enzyme_format.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Map/
 lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Map/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Map/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Map/map_format.py
-lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Map/map_format.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Kabat/
-lib/python${MODPY_VERSION}/site-packages/Bio/Kabat/Record.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Kabat/Record.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Kabat/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Kabat/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Kabat/kabat_format.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Kabat/kabat_format.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/LocusLink/
 lib/python${MODPY_VERSION}/site-packages/Bio/LocusLink/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/LocusLink/__init__.pyc
@@ -490,6 +481,8 @@ lib/python${MODPY_VERSION}/site-packages/Bio/PDB/PDBList.py
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/PDBList.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/PDBParser.py
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/PDBParser.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/PDB/PSEA.py
+lib/python${MODPY_VERSION}/site-packages/Bio/PDB/PSEA.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/Polypeptide.py
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/Polypeptide.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/Residue.py
@@ -511,7 +504,6 @@ lib/python${MODPY_VERSION}/site-packages/Bio/PDB/Vector.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/mmCIF/
-lib/python${MODPY_VERSION}/site-packages/Bio/PDB/mmCIF/MMCIFlex.so
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/mmCIF/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/mmCIF/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/parse_pdb_header.py
@@ -535,6 +527,28 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Pathway/Rep/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Pathway/Rep/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Pathway/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Pathway/__init__.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/Async/
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/Async/Local.py
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/Async/Local.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/Async/__init__.py
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/Async/__init__.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/FDist/
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/FDist/Async.py
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/FDist/Async.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/FDist/Controller.py
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/FDist/Controller.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/FDist/Utils.py
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/FDist/Utils.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/FDist/__init__.py
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/FDist/__init__.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/GenePop/
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/GenePop/Utils.py
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/GenePop/Utils.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/GenePop/__init__.py
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/GenePop/__init__.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/__init__.py
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/PropertyManager.py
 lib/python${MODPY_VERSION}/site-packages/Bio/PropertyManager.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Prosite/
@@ -549,10 +563,6 @@ lib/python${MODPY_VERSION}/site-packages/Bio/PubMed.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Rebase/
 lib/python${MODPY_VERSION}/site-packages/Bio/Rebase/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Rebase/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/RecordFile.py
-lib/python${MODPY_VERSION}/site-packages/Bio/RecordFile.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/ReseekFile.py
-lib/python${MODPY_VERSION}/site-packages/Bio/ReseekFile.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Restriction/
 lib/python${MODPY_VERSION}/site-packages/Bio/Restriction/DNAUtils.so
 lib/python${MODPY_VERSION}/site-packages/Bio/Restriction/PrintFormat.py
@@ -596,8 +606,6 @@ lib/python${MODPY_VERSION}/site-packages/Bio/SVDSuperimposer/SVDSuperimposer.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SVDSuperimposer/SVDSuperimposer.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SVDSuperimposer/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SVDSuperimposer/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/SVM.py
-lib/python${MODPY_VERSION}/site-packages/Bio/SVM.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Saf/
 lib/python${MODPY_VERSION}/site-packages/Bio/Saf/Record.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Saf/Record.pyc
@@ -612,8 +620,24 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Seq.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqFeature.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqFeature.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/ClustalIO.py
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/ClustalIO.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/FASTA.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/FASTA.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/FastaIO.py
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/FastaIO.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/InsdcIO.py
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/InsdcIO.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/Interfaces.py
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/Interfaces.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/NexusIO.py
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/NexusIO.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/PhylipIO.py
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/PhylipIO.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/StockholmIO.py
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/StockholmIO.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/SwissIO.py
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/SwissIO.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/generic.py
@@ -621,6 +645,8 @@ lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/generic.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqRecord.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqRecord.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/CheckSum.py
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/CheckSum.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/CodonUsage.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/CodonUsage.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/CodonUsageIndices.py
@@ -635,6 +661,8 @@ lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/ProtParamData.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/ProtParamData.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/__init__.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/lcc.py
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/lcc.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/
 lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/Ace.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/Ace.pyc
@@ -710,9 +738,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/builders/SeqRecord/sequence.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/builders/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/builders/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/cMarkovModel.so
-lib/python${MODPY_VERSION}/site-packages/Bio/cSVM.so
 lib/python${MODPY_VERSION}/site-packages/Bio/cdistance.so
-lib/python${MODPY_VERSION}/site-packages/Bio/ckMeans.so
 lib/python${MODPY_VERSION}/site-packages/Bio/clistfns.so
 lib/python${MODPY_VERSION}/site-packages/Bio/cmathfns.so
 lib/python${MODPY_VERSION}/site-packages/Bio/config/
@@ -808,8 +834,6 @@ lib/python${MODPY_VERSION}/site-packages/Bio/formatdefs/sequence.py
 lib/python${MODPY_VERSION}/site-packages/Bio/formatdefs/sequence.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/formatdefs/swissprot.py
 lib/python${MODPY_VERSION}/site-packages/Bio/formatdefs/swissprot.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/kMeans.py
-lib/python${MODPY_VERSION}/site-packages/Bio/kMeans.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/kNN.py
 lib/python${MODPY_VERSION}/site-packages/Bio/kNN.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/lcc.py
@@ -820,8 +844,6 @@ lib/python${MODPY_VERSION}/site-packages/Bio/mathfns.py
 lib/python${MODPY_VERSION}/site-packages/Bio/mathfns.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/pairwise2.py
 lib/python${MODPY_VERSION}/site-packages/Bio/pairwise2.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/sequtils.py
-lib/python${MODPY_VERSION}/site-packages/Bio/sequtils.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/stringfns.py
 lib/python${MODPY_VERSION}/site-packages/Bio/stringfns.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/trie.so
@@ -841,8 +863,6 @@ lib/python${MODPY_VERSION}/site-packages/Bio/writers/SeqRecord/fasta.py
 lib/python${MODPY_VERSION}/site-packages/Bio/writers/SeqRecord/fasta.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/writers/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/writers/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/xkMeans.py
-lib/python${MODPY_VERSION}/site-packages/Bio/xkMeans.pyc
 lib/python${MODPY_VERSION}/site-packages/BioSQL/
 lib/python${MODPY_VERSION}/site-packages/BioSQL/BioSeq.py
 lib/python${MODPY_VERSION}/site-packages/BioSQL/BioSeq.pyc
@@ -885,622 +905,35 @@ lib/python${MODPY_VERSION}/site-packages/Martel/optimize.py
 lib/python${MODPY_VERSION}/site-packages/Martel/optimize.pyc
 @comment lib/python${MODPY_VERSION}/site-packages/Martel/setup.py
 @comment lib/python${MODPY_VERSION}/site-packages/Martel/setup.pyc
-lib/python${MODPY_VERSION}/site-packages/biopython-1.41-py${MODPY_VERSION}.egg-info
+lib/python${MODPY_VERSION}/site-packages/biopython-1.44-py${MODPY_VERSION}.egg-info
+share/doc/py-biopython/
+share/doc/py-biopython/CDD.txt
+share/doc/py-biopython/Crystal.txt
+share/doc/py-biopython/ECell.txt
+share/doc/py-biopython/FilteredReader.txt
+share/doc/py-biopython/Geo.txt
+share/doc/py-biopython/IntelliGenetics.txt
+share/doc/py-biopython/InterPro.txt
+share/doc/py-biopython/NetCatch.txt
+share/doc/py-biopython/References.txt
+share/doc/py-biopython/SGMLExtractor.txt
+share/doc/py-biopython/Saf.txt
+share/doc/py-biopython/Tutorial.txt
 share/examples/py-biopython/
-share/examples/py-biopython/Ace/
-share/examples/py-biopython/Ace/contig1.ace
-share/examples/py-biopython/Amino/
-share/examples/py-biopython/Amino/aster.pro
-share/examples/py-biopython/Amino/loveliesbleeding.pro
-share/examples/py-biopython/Amino/rose.pro
-share/examples/py-biopython/Amino/rosemary.pro
-share/examples/py-biopython/BioSQL/
-share/examples/py-biopython/BioSQL/biosqldb-mysql.sql
-share/examples/py-biopython/BioSQL/biosqldb-pg.sql
-share/examples/py-biopython/Blast/
-share/examples/py-biopython/Blast/README
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-share/examples/py-biopython/CodonUsage/
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-share/examples/py-biopython/Emboss/cds_forward.primer3
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-share/examples/py-biopython/Geo/GSM645.txt
-share/examples/py-biopython/Geo/GSM691.txt
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