4 files changed, 886 insertions, 0 deletions

diff --git a/biology/pycogent/Makefile b/biology/pycogent/Makefile
new file mode 100644
index 000000000000..4b8348554b0d
--- /dev/null
+++ b/biology/pycogent/Makefile
@@ -0,0 +1,28 @@
+# New ports collection makefile for:	pycogent
+# Date created:		20 June, 2009
+# Whom:			Wen Heping <wenheping@gmail.com>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	pycogent
+PORTVERSION=	1.3.1
+CATEGORIES=	biology python
+MASTER_SITES=	SF
+DISTNAME=	PyCogent-${PORTVERSION}
+EXTRACT_SUFX=	.tgz
+
+MAINTAINER=	wenheping@gmail.com
+COMMENT=	A toolkit for statistical analysis of biological sequences
+
+BUILD_DEPENDS=	${PYNUMPY} \
+		${LOCALBASE}/bin/cython:${PORTSDIR}/lang/cython \
+		${LOCALBASE}/bin/sphinx-build:${PORTSDIR}/textproc/py-sphinx \
+		${PYTHON_PKGNAMEPREFIX}sqlalchemy>=0.5:${PORTSDIR}/databases/py-sqlalchemy
+RUN_DEPENDS=	${BUILD_DEPENDS}
+
+USE_PYTHON=		yes
+USE_PYDISTUTILS=	yes
+PYDISTUTILS_PKGNAME=	cogent
+
+.include <bsd.port.mk>
diff --git a/biology/pycogent/distinfo b/biology/pycogent/distinfo
new file mode 100644
index 000000000000..09398220a025
--- /dev/null
+++ b/biology/pycogent/distinfo
@@ -0,0 +1,3 @@
+MD5 (PyCogent-1.3.1.tgz) = 4cc108a69e5ffd343508db4615514b74
+SHA256 (PyCogent-1.3.1.tgz) = 56636a2aeee464968056458f8384262f874cdac12b89a43c4c3e5d88582a7fc6
+SIZE (PyCogent-1.3.1.tgz) = 2062874
diff --git a/biology/pycogent/pkg-descr b/biology/pycogent/pkg-descr
new file mode 100644
index 000000000000..600342b93248
--- /dev/null
+++ b/biology/pycogent/pkg-descr
@@ -0,0 +1,9 @@
+PyCogent is a software library for genomic biology. It is a fully integrated
+and thoroughly tested framework for: controlling third-party applications;
+devising workflows; querying databases; conducting novel probabilistic
+analyses of biological sequence evolution; and generating publication quality
+graphics. It is distinguished by many unique built-in capabilities (such as
+true codon alignment) and the frequent addition of entirely new methods for
+the analysis of genomic data.
+
+WWW:	http://pycogent.sourceforge.net/
diff --git a/biology/pycogent/pkg-plist b/biology/pycogent/pkg-plist
new file mode 100644
index 000000000000..a1bc29f1f35d
--- /dev/null
+++ b/biology/pycogent/pkg-plist
@@ -0,0 +1,846 @@
+%%PYTHON_SITELIBDIR%%/cogent/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/align/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/_compare.so
+%%PYTHON_SITELIBDIR%%/cogent/align/_pairwise_pogs.so
+%%PYTHON_SITELIBDIR%%/cogent/align/_pairwise_seqs.so
+%%PYTHON_SITELIBDIR%%/cogent/align/algorithm.py
+%%PYTHON_SITELIBDIR%%/cogent/align/algorithm.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/algorithm.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/align.py
+%%PYTHON_SITELIBDIR%%/cogent/align/align.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/align.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/dp_calculation.py
+%%PYTHON_SITELIBDIR%%/cogent/align/dp_calculation.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/dp_calculation.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/indel_model.py
+%%PYTHON_SITELIBDIR%%/cogent/align/indel_model.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/indel_model.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/indel_positions.py
+%%PYTHON_SITELIBDIR%%/cogent/align/indel_positions.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/indel_positions.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/pairwise.py
+%%PYTHON_SITELIBDIR%%/cogent/align/pairwise.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/pairwise.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/partial_order_graph.py
+%%PYTHON_SITELIBDIR%%/cogent/align/partial_order_graph.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/partial_order_graph.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/progressive.py
+%%PYTHON_SITELIBDIR%%/cogent/align/progressive.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/progressive.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/pycompare.py
+%%PYTHON_SITELIBDIR%%/cogent/align/pycompare.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/pycompare.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/traceback.py
+%%PYTHON_SITELIBDIR%%/cogent/align/traceback.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/traceback.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/weights/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/align/weights/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/weights/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/weights/methods.py
+%%PYTHON_SITELIBDIR%%/cogent/align/weights/methods.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/weights/methods.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/weights/util.py
+%%PYTHON_SITELIBDIR%%/cogent/align/weights/util.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/weights/util.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/app/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/blast.py
+%%PYTHON_SITELIBDIR%%/cogent/app/blast.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/blast.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/carnac.py
+%%PYTHON_SITELIBDIR%%/cogent/app/carnac.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/carnac.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/cd_hit.py
+%%PYTHON_SITELIBDIR%%/cogent/app/cd_hit.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/cd_hit.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/clearcut.py
+%%PYTHON_SITELIBDIR%%/cogent/app/clearcut.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/clearcut.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/clustalw.py
+%%PYTHON_SITELIBDIR%%/cogent/app/clustalw.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/clustalw.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/cmfinder.py
+%%PYTHON_SITELIBDIR%%/cogent/app/cmfinder.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/cmfinder.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/comrna.py
+%%PYTHON_SITELIBDIR%%/cogent/app/comrna.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/comrna.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/consan.py
+%%PYTHON_SITELIBDIR%%/cogent/app/consan.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/consan.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/contrafold.py
+%%PYTHON_SITELIBDIR%%/cogent/app/contrafold.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/contrafold.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/cove.py
+%%PYTHON_SITELIBDIR%%/cogent/app/cove.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/cove.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/dialign.py
+%%PYTHON_SITELIBDIR%%/cogent/app/dialign.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/dialign.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/dotur.py
+%%PYTHON_SITELIBDIR%%/cogent/app/dotur.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/dotur.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/dynalign.py
+%%PYTHON_SITELIBDIR%%/cogent/app/dynalign.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/dynalign.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/fasttree.py
+%%PYTHON_SITELIBDIR%%/cogent/app/fasttree.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/fasttree.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/fasttree_v1.py
+%%PYTHON_SITELIBDIR%%/cogent/app/fasttree_v1.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/fasttree_v1.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/foldalign.py
+%%PYTHON_SITELIBDIR%%/cogent/app/foldalign.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/foldalign.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/gctmpca.py
+%%PYTHON_SITELIBDIR%%/cogent/app/gctmpca.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/gctmpca.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/ilm.py
+%%PYTHON_SITELIBDIR%%/cogent/app/ilm.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/ilm.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/infernal.py
+%%PYTHON_SITELIBDIR%%/cogent/app/infernal.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/infernal.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/knetfold.py
+%%PYTHON_SITELIBDIR%%/cogent/app/knetfold.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/knetfold.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/lagan.py
+%%PYTHON_SITELIBDIR%%/cogent/app/lagan.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/lagan.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/mafft.py
+%%PYTHON_SITELIBDIR%%/cogent/app/mafft.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/mafft.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/mfold.py
+%%PYTHON_SITELIBDIR%%/cogent/app/mfold.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/mfold.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/muscle.py
+%%PYTHON_SITELIBDIR%%/cogent/app/muscle.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/muscle.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/nupack.py
+%%PYTHON_SITELIBDIR%%/cogent/app/nupack.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/nupack.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/parameters.py
+%%PYTHON_SITELIBDIR%%/cogent/app/parameters.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/parameters.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/pfold.py
+%%PYTHON_SITELIBDIR%%/cogent/app/pfold.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/pfold.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/pknotsrg.py
+%%PYTHON_SITELIBDIR%%/cogent/app/pknotsrg.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/pknotsrg.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/raxml.py
+%%PYTHON_SITELIBDIR%%/cogent/app/raxml.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/raxml.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/rnaalifold.py
+%%PYTHON_SITELIBDIR%%/cogent/app/rnaalifold.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/rnaalifold.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/rnaforester.py
+%%PYTHON_SITELIBDIR%%/cogent/app/rnaforester.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/rnaforester.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/rnashapes.py
+%%PYTHON_SITELIBDIR%%/cogent/app/rnashapes.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/rnashapes.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/rnaview.py
+%%PYTHON_SITELIBDIR%%/cogent/app/rnaview.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/rnaview.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/sfold.py
+%%PYTHON_SITELIBDIR%%/cogent/app/sfold.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/sfold.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/unafold.py
+%%PYTHON_SITELIBDIR%%/cogent/app/unafold.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/unafold.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/util.py
+%%PYTHON_SITELIBDIR%%/cogent/app/util.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/util.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/vienna_package.py
+%%PYTHON_SITELIBDIR%%/cogent/app/vienna_package.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/vienna_package.pyo
+%%PYTHON_SITELIBDIR%%/cogent/cluster/UPGMA.py
+%%PYTHON_SITELIBDIR%%/cogent/cluster/UPGMA.pyc
+%%PYTHON_SITELIBDIR%%/cogent/cluster/UPGMA.pyo
+%%PYTHON_SITELIBDIR%%/cogent/cluster/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/cluster/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/cluster/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/cluster/metric_scaling.py
+%%PYTHON_SITELIBDIR%%/cogent/cluster/metric_scaling.pyc
+%%PYTHON_SITELIBDIR%%/cogent/cluster/metric_scaling.pyo
+%%PYTHON_SITELIBDIR%%/cogent/cluster/nmds.py
+%%PYTHON_SITELIBDIR%%/cogent/cluster/nmds.pyc
+%%PYTHON_SITELIBDIR%%/cogent/cluster/nmds.pyo
+%%PYTHON_SITELIBDIR%%/cogent/core/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/core/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/core/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/core/alignment.py
+%%PYTHON_SITELIBDIR%%/cogent/core/alignment.pyc
+%%PYTHON_SITELIBDIR%%/cogent/core/alignment.pyo
+%%PYTHON_SITELIBDIR%%/cogent/core/alphabet.py
+%%PYTHON_SITELIBDIR%%/cogent/core/alphabet.pyc
+%%PYTHON_SITELIBDIR%%/cogent/core/alphabet.pyo
+%%PYTHON_SITELIBDIR%%/cogent/core/annotation.py
+%%PYTHON_SITELIBDIR%%/cogent/core/annotation.pyc
+%%PYTHON_SITELIBDIR%%/cogent/core/annotation.pyo
+%%PYTHON_SITELIBDIR%%/cogent/core/bitvector.py
+%%PYTHON_SITELIBDIR%%/cogent/core/bitvector.pyc
+%%PYTHON_SITELIBDIR%%/cogent/core/bitvector.pyo
+%%PYTHON_SITELIBDIR%%/cogent/core/genetic_code.py
+%%PYTHON_SITELIBDIR%%/cogent/core/genetic_code.pyc
+%%PYTHON_SITELIBDIR%%/cogent/core/genetic_code.pyo
+%%PYTHON_SITELIBDIR%%/cogent/core/info.py
+%%PYTHON_SITELIBDIR%%/cogent/core/info.pyc
+%%PYTHON_SITELIBDIR%%/cogent/core/info.pyo
+%%PYTHON_SITELIBDIR%%/cogent/core/location.py
+%%PYTHON_SITELIBDIR%%/cogent/core/location.pyc
+%%PYTHON_SITELIBDIR%%/cogent/core/location.pyo
+%%PYTHON_SITELIBDIR%%/cogent/core/moltype.py
+%%PYTHON_SITELIBDIR%%/cogent/core/moltype.pyc
+%%PYTHON_SITELIBDIR%%/cogent/core/moltype.pyo
+%%PYTHON_SITELIBDIR%%/cogent/core/profile.py
+%%PYTHON_SITELIBDIR%%/cogent/core/profile.pyc
+%%PYTHON_SITELIBDIR%%/cogent/core/profile.pyo
+%%PYTHON_SITELIBDIR%%/cogent/core/sequence.py
+%%PYTHON_SITELIBDIR%%/cogent/core/sequence.pyc
+%%PYTHON_SITELIBDIR%%/cogent/core/sequence.pyo
+%%PYTHON_SITELIBDIR%%/cogent/core/tree.py
+%%PYTHON_SITELIBDIR%%/cogent/core/tree.pyc
+%%PYTHON_SITELIBDIR%%/cogent/core/tree.pyo
+%%PYTHON_SITELIBDIR%%/cogent/core/usage.py
+%%PYTHON_SITELIBDIR%%/cogent/core/usage.pyc
+%%PYTHON_SITELIBDIR%%/cogent/core/usage.pyo
+%%PYTHON_SITELIBDIR%%/cogent/data/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/data/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/data/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/data/energy_params.py
+%%PYTHON_SITELIBDIR%%/cogent/data/energy_params.pyc
+%%PYTHON_SITELIBDIR%%/cogent/data/energy_params.pyo
+%%PYTHON_SITELIBDIR%%/cogent/data/molecular_weight.py
+%%PYTHON_SITELIBDIR%%/cogent/data/molecular_weight.pyc
+%%PYTHON_SITELIBDIR%%/cogent/data/molecular_weight.pyo
+%%PYTHON_SITELIBDIR%%/cogent/db/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/db/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/db/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/assembly.py
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/assembly.pyc
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/assembly.pyo
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/compara.py
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/compara.pyc
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/compara.pyo
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/database.py
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/database.pyc
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/database.pyo
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/feature_level.py
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/feature_level.pyc
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/feature_level.pyo
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/genome.py
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/genome.pyc
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/genome.pyo
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/host.py
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/host.pyc
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/host.pyo
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/name.py
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/name.pyc
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/name.pyo
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/region.py
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/region.pyc
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/region.pyo
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/related_region.py
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/related_region.pyc
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/related_region.pyo
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/sequence.py
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/sequence.pyc
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/sequence.pyo
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/species.py
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/species.pyc
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/species.pyo
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/util.py
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/util.pyc
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/util.pyo
+%%PYTHON_SITELIBDIR%%/cogent/db/ncbi.py
+%%PYTHON_SITELIBDIR%%/cogent/db/ncbi.pyc
+%%PYTHON_SITELIBDIR%%/cogent/db/ncbi.pyo
+%%PYTHON_SITELIBDIR%%/cogent/db/pdb.py
+%%PYTHON_SITELIBDIR%%/cogent/db/pdb.pyc
+%%PYTHON_SITELIBDIR%%/cogent/db/pdb.pyo
+%%PYTHON_SITELIBDIR%%/cogent/db/rfam.py
+%%PYTHON_SITELIBDIR%%/cogent/db/rfam.pyc
+%%PYTHON_SITELIBDIR%%/cogent/db/rfam.pyo
+%%PYTHON_SITELIBDIR%%/cogent/db/util.py
+%%PYTHON_SITELIBDIR%%/cogent/db/util.pyc
+%%PYTHON_SITELIBDIR%%/cogent/db/util.pyo
+%%PYTHON_SITELIBDIR%%/cogent/draw/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/draw/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/draw/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/draw/dendrogram.py
+%%PYTHON_SITELIBDIR%%/cogent/draw/dendrogram.pyc
+%%PYTHON_SITELIBDIR%%/cogent/draw/dendrogram.pyo
+%%PYTHON_SITELIBDIR%%/cogent/draw/dotplot.py
+%%PYTHON_SITELIBDIR%%/cogent/draw/dotplot.pyc
+%%PYTHON_SITELIBDIR%%/cogent/draw/dotplot.pyo
+%%PYTHON_SITELIBDIR%%/cogent/draw/legend.py
+%%PYTHON_SITELIBDIR%%/cogent/draw/legend.pyc
+%%PYTHON_SITELIBDIR%%/cogent/draw/legend.pyo
+%%PYTHON_SITELIBDIR%%/cogent/draw/linear.py
+%%PYTHON_SITELIBDIR%%/cogent/draw/linear.pyc
+%%PYTHON_SITELIBDIR%%/cogent/draw/linear.pyo
+%%PYTHON_SITELIBDIR%%/cogent/draw/matplotlib/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/draw/matplotlib/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/draw/matplotlib/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/draw/matplotlib/arrow_rates.py
+%%PYTHON_SITELIBDIR%%/cogent/draw/matplotlib/arrow_rates.pyc
+%%PYTHON_SITELIBDIR%%/cogent/draw/matplotlib/arrow_rates.pyo
+%%PYTHON_SITELIBDIR%%/cogent/draw/matplotlib/codon_usage.py
+%%PYTHON_SITELIBDIR%%/cogent/draw/matplotlib/codon_usage.pyc
+%%PYTHON_SITELIBDIR%%/cogent/draw/matplotlib/codon_usage.pyo
+%%PYTHON_SITELIBDIR%%/cogent/draw/matplotlib/dinuc.py
+%%PYTHON_SITELIBDIR%%/cogent/draw/matplotlib/dinuc.pyc
+%%PYTHON_SITELIBDIR%%/cogent/draw/matplotlib/dinuc.pyo
+%%PYTHON_SITELIBDIR%%/cogent/draw/matplotlib/fancy_arrow.py
+%%PYTHON_SITELIBDIR%%/cogent/draw/matplotlib/fancy_arrow.pyc
+%%PYTHON_SITELIBDIR%%/cogent/draw/matplotlib/fancy_arrow.pyo
+%%PYTHON_SITELIBDIR%%/cogent/draw/matplotlib/multivariate_plot.py
+%%PYTHON_SITELIBDIR%%/cogent/draw/matplotlib/multivariate_plot.pyc
+%%PYTHON_SITELIBDIR%%/cogent/draw/matplotlib/multivariate_plot.pyo
+%%PYTHON_SITELIBDIR%%/cogent/draw/matplotlib/util.py
+%%PYTHON_SITELIBDIR%%/cogent/draw/matplotlib/util.pyc
+%%PYTHON_SITELIBDIR%%/cogent/draw/matplotlib/util.pyo
+%%PYTHON_SITELIBDIR%%/cogent/evolve/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/evolve/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/evolve/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/evolve/_likelihood_tree.so
+%%PYTHON_SITELIBDIR%%/cogent/evolve/best_likelihood.py
+%%PYTHON_SITELIBDIR%%/cogent/evolve/best_likelihood.pyc
+%%PYTHON_SITELIBDIR%%/cogent/evolve/best_likelihood.pyo
+%%PYTHON_SITELIBDIR%%/cogent/evolve/bootstrap.py
+%%PYTHON_SITELIBDIR%%/cogent/evolve/bootstrap.pyc
+%%PYTHON_SITELIBDIR%%/cogent/evolve/bootstrap.pyo
+%%PYTHON_SITELIBDIR%%/cogent/evolve/coevolution.py
+%%PYTHON_SITELIBDIR%%/cogent/evolve/coevolution.pyc
+%%PYTHON_SITELIBDIR%%/cogent/evolve/coevolution.pyo
+%%PYTHON_SITELIBDIR%%/cogent/evolve/likelihood_calculation.py
+%%PYTHON_SITELIBDIR%%/cogent/evolve/likelihood_calculation.pyc
+%%PYTHON_SITELIBDIR%%/cogent/evolve/likelihood_calculation.pyo
+%%PYTHON_SITELIBDIR%%/cogent/evolve/likelihood_function.py
+%%PYTHON_SITELIBDIR%%/cogent/evolve/likelihood_function.pyc
+%%PYTHON_SITELIBDIR%%/cogent/evolve/likelihood_function.pyo
+%%PYTHON_SITELIBDIR%%/cogent/evolve/likelihood_tree.py
+%%PYTHON_SITELIBDIR%%/cogent/evolve/likelihood_tree.pyc
+%%PYTHON_SITELIBDIR%%/cogent/evolve/likelihood_tree.pyo
+%%PYTHON_SITELIBDIR%%/cogent/evolve/models.py
+%%PYTHON_SITELIBDIR%%/cogent/evolve/models.pyc
+%%PYTHON_SITELIBDIR%%/cogent/evolve/models.pyo
+%%PYTHON_SITELIBDIR%%/cogent/evolve/parameter_controller.py
+%%PYTHON_SITELIBDIR%%/cogent/evolve/parameter_controller.pyc
+%%PYTHON_SITELIBDIR%%/cogent/evolve/parameter_controller.pyo
+%%PYTHON_SITELIBDIR%%/cogent/evolve/predicate.py
+%%PYTHON_SITELIBDIR%%/cogent/evolve/predicate.pyc
+%%PYTHON_SITELIBDIR%%/cogent/evolve/predicate.pyo
+%%PYTHON_SITELIBDIR%%/cogent/evolve/simulate.py
+%%PYTHON_SITELIBDIR%%/cogent/evolve/simulate.pyc
+%%PYTHON_SITELIBDIR%%/cogent/evolve/simulate.pyo
+%%PYTHON_SITELIBDIR%%/cogent/evolve/substitution_calculation.py
+%%PYTHON_SITELIBDIR%%/cogent/evolve/substitution_calculation.pyc
+%%PYTHON_SITELIBDIR%%/cogent/evolve/substitution_calculation.pyo
+%%PYTHON_SITELIBDIR%%/cogent/evolve/substitution_model.py
+%%PYTHON_SITELIBDIR%%/cogent/evolve/substitution_model.pyc
+%%PYTHON_SITELIBDIR%%/cogent/evolve/substitution_model.pyo
+%%PYTHON_SITELIBDIR%%/cogent/format/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/format/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/format/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/format/alignment.py
+%%PYTHON_SITELIBDIR%%/cogent/format/alignment.pyc
+%%PYTHON_SITELIBDIR%%/cogent/format/alignment.pyo
+%%PYTHON_SITELIBDIR%%/cogent/format/clustal.py
+%%PYTHON_SITELIBDIR%%/cogent/format/clustal.pyc
+%%PYTHON_SITELIBDIR%%/cogent/format/clustal.pyo
+%%PYTHON_SITELIBDIR%%/cogent/format/fasta.py
+%%PYTHON_SITELIBDIR%%/cogent/format/fasta.pyc
+%%PYTHON_SITELIBDIR%%/cogent/format/fasta.pyo
+%%PYTHON_SITELIBDIR%%/cogent/format/mage.py
+%%PYTHON_SITELIBDIR%%/cogent/format/mage.pyc
+%%PYTHON_SITELIBDIR%%/cogent/format/mage.pyo
+%%PYTHON_SITELIBDIR%%/cogent/format/motif.py
+%%PYTHON_SITELIBDIR%%/cogent/format/motif.pyc
+%%PYTHON_SITELIBDIR%%/cogent/format/motif.pyo
+%%PYTHON_SITELIBDIR%%/cogent/format/nexus.py
+%%PYTHON_SITELIBDIR%%/cogent/format/nexus.pyc
+%%PYTHON_SITELIBDIR%%/cogent/format/nexus.pyo
+%%PYTHON_SITELIBDIR%%/cogent/format/pdb_color.py
+%%PYTHON_SITELIBDIR%%/cogent/format/pdb_color.pyc
+%%PYTHON_SITELIBDIR%%/cogent/format/pdb_color.pyo
+%%PYTHON_SITELIBDIR%%/cogent/format/phylip.py
+%%PYTHON_SITELIBDIR%%/cogent/format/phylip.pyc
+%%PYTHON_SITELIBDIR%%/cogent/format/phylip.pyo
+%%PYTHON_SITELIBDIR%%/cogent/format/rna_struct.py
+%%PYTHON_SITELIBDIR%%/cogent/format/rna_struct.pyc
+%%PYTHON_SITELIBDIR%%/cogent/format/rna_struct.pyo
+%%PYTHON_SITELIBDIR%%/cogent/format/stockholm.py
+%%PYTHON_SITELIBDIR%%/cogent/format/stockholm.pyc
+%%PYTHON_SITELIBDIR%%/cogent/format/stockholm.pyo
+%%PYTHON_SITELIBDIR%%/cogent/format/table.py
+%%PYTHON_SITELIBDIR%%/cogent/format/table.pyc
+%%PYTHON_SITELIBDIR%%/cogent/format/table.pyo
+%%PYTHON_SITELIBDIR%%/cogent/format/text_tree.py
+%%PYTHON_SITELIBDIR%%/cogent/format/text_tree.pyc
+%%PYTHON_SITELIBDIR%%/cogent/format/text_tree.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/_matrix_exponentiation.so
+%%PYTHON_SITELIBDIR%%/cogent/maths/distance_transform.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/distance_transform.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/distance_transform.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/function_optimisation.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/function_optimisation.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/function_optimisation.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/geometry.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/geometry.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/geometry.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/markov.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/markov.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/markov.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/matrix/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/matrix/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/matrix/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/matrix/distance.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/matrix/distance.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/matrix/distance.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/matrix_exponentiation.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/matrix_exponentiation.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/matrix_exponentiation.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/matrix_logarithm.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/matrix_logarithm.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/matrix_logarithm.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/optimiser.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/optimiser.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/optimiser.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/optimisers.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/optimisers.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/optimisers.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/scipy_optimisers.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/scipy_optimisers.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/scipy_optimisers.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/scipy_optimize.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/scipy_optimize.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/scipy_optimize.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/simannealingoptimiser.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/simannealingoptimiser.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/simannealingoptimiser.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/solve.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/solve.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/solve.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/adaptor.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/adaptor.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/adaptor.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/get_by_cai.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/get_by_cai.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/get_by_cai.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/util.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/util.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/util.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/distribution.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/distribution.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/distribution.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/histogram.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/histogram.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/histogram.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/kendall.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/kendall.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/kendall.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/ks.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/ks.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/ks.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/special.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/special.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/special.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/test.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/test.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/test.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/util.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/util.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/util.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/svd.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/svd.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/svd.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/unifrac/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/unifrac/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/unifrac/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/unifrac/fast_tree.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/unifrac/fast_tree.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/unifrac/fast_tree.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/unifrac/fast_unifrac.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/unifrac/fast_unifrac.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/unifrac/fast_unifrac.pyo
+%%PYTHON_SITELIBDIR%%/cogent/motif/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/motif/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/motif/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/motif/k_word.py
+%%PYTHON_SITELIBDIR%%/cogent/motif/k_word.pyc
+%%PYTHON_SITELIBDIR%%/cogent/motif/k_word.pyo
+%%PYTHON_SITELIBDIR%%/cogent/motif/util.py
+%%PYTHON_SITELIBDIR%%/cogent/motif/util.pyc
+%%PYTHON_SITELIBDIR%%/cogent/motif/util.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/aaindex.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/aaindex.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/aaindex.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/agilent_microarray.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/agilent_microarray.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/agilent_microarray.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/blast.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/blast.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/blast.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/bpseq.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/bpseq.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/bpseq.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/carnac.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/carnac.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/carnac.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/cigar.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/cigar.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/cigar.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/clustal.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/clustal.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/clustal.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/cmfinder.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/cmfinder.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/cmfinder.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/column.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/column.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/column.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/comrna.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/comrna.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/comrna.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/consan.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/consan.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/consan.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/contrafold.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/contrafold.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/contrafold.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/cove.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/cove.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/cove.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/ct.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/ct.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/ct.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/cut.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/cut.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/cut.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/cutg.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/cutg.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/cutg.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/dialign.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/dialign.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/dialign.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/dotur.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/dotur.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/dotur.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/dynalign.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/dynalign.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/dynalign.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/ebi.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/ebi.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/ebi.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/fasta.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/fasta.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/fasta.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/foldalign.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/foldalign.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/foldalign.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/gbseq.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/gbseq.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/gbseq.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/gcg.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/gcg.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/gcg.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/genbank.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/genbank.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/genbank.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/gff.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/gff.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/gff.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/gibbs.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/gibbs.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/gibbs.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/ilm.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/ilm.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/ilm.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/infernal.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/infernal.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/infernal.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/knetfold.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/knetfold.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/knetfold.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/locuslink.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/locuslink.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/locuslink.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/macsim.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/macsim.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/macsim.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/mage.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/mage.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/mage.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/meme.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/meme.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/meme.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/mfold.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/mfold.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/mfold.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/ncbi_taxonomy.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/ncbi_taxonomy.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/ncbi_taxonomy.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/newick.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/newick.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/newick.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/nexus.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/nexus.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/nexus.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/nupack.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/nupack.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/nupack.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/paml.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/paml.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/paml.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/paml_matrix.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/paml_matrix.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/paml_matrix.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/pfold.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/pfold.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/pfold.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/phylip.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/phylip.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/phylip.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/pknotsrg.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/pknotsrg.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/pknotsrg.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/rdb.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/rdb.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/rdb.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/record.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/record.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/record.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/record_finder.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/record_finder.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/record_finder.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/rfam.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/rfam.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/rfam.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/rna_fold.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/rna_fold.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/rna_fold.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/rna_plot.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/rna_plot.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/rna_plot.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/rnaalifold.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/rnaalifold.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/rnaalifold.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/rnaforester.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/rnaforester.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/rnaforester.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/rnashapes.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/rnashapes.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/rnashapes.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/rnaview.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/rnaview.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/rnaview.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/sequence.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/sequence.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/sequence.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/sfold.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/sfold.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/sfold.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/sprinzl.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/sprinzl.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/sprinzl.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/table.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/table.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/table.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/tinyseq.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/tinyseq.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/tinyseq.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/tree.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/tree.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/tree.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/tree_xml.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/tree_xml.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/tree_xml.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/unafold.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/unafold.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/unafold.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/unigene.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/unigene.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/unigene.pyo
+%%PYTHON_SITELIBDIR%%/cogent/phylo/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/phylo/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/phylo/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/phylo/consensus.py
+%%PYTHON_SITELIBDIR%%/cogent/phylo/consensus.pyc
+%%PYTHON_SITELIBDIR%%/cogent/phylo/consensus.pyo
+%%PYTHON_SITELIBDIR%%/cogent/phylo/distance.py
+%%PYTHON_SITELIBDIR%%/cogent/phylo/distance.pyc
+%%PYTHON_SITELIBDIR%%/cogent/phylo/distance.pyo
+%%PYTHON_SITELIBDIR%%/cogent/phylo/least_squares.py
+%%PYTHON_SITELIBDIR%%/cogent/phylo/least_squares.pyc
+%%PYTHON_SITELIBDIR%%/cogent/phylo/least_squares.pyo
+%%PYTHON_SITELIBDIR%%/cogent/phylo/maximum_likelihood.py
+%%PYTHON_SITELIBDIR%%/cogent/phylo/maximum_likelihood.pyc
+%%PYTHON_SITELIBDIR%%/cogent/phylo/maximum_likelihood.pyo
+%%PYTHON_SITELIBDIR%%/cogent/phylo/nj.py
+%%PYTHON_SITELIBDIR%%/cogent/phylo/nj.pyc
+%%PYTHON_SITELIBDIR%%/cogent/phylo/nj.pyo
+%%PYTHON_SITELIBDIR%%/cogent/phylo/tree_space.py
+%%PYTHON_SITELIBDIR%%/cogent/phylo/tree_space.pyc
+%%PYTHON_SITELIBDIR%%/cogent/phylo/tree_space.pyo
+%%PYTHON_SITELIBDIR%%/cogent/phylo/util.py
+%%PYTHON_SITELIBDIR%%/cogent/phylo/util.pyc
+%%PYTHON_SITELIBDIR%%/cogent/phylo/util.pyo
+%%PYTHON_SITELIBDIR%%/cogent/recalculation/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/recalculation/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/recalculation/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/recalculation/calculation.py
+%%PYTHON_SITELIBDIR%%/cogent/recalculation/calculation.pyc
+%%PYTHON_SITELIBDIR%%/cogent/recalculation/calculation.pyo
+%%PYTHON_SITELIBDIR%%/cogent/recalculation/definition.py
+%%PYTHON_SITELIBDIR%%/cogent/recalculation/definition.pyc
+%%PYTHON_SITELIBDIR%%/cogent/recalculation/definition.pyo
+%%PYTHON_SITELIBDIR%%/cogent/recalculation/scope.py
+%%PYTHON_SITELIBDIR%%/cogent/recalculation/scope.pyc
+%%PYTHON_SITELIBDIR%%/cogent/recalculation/scope.pyo
+%%PYTHON_SITELIBDIR%%/cogent/recalculation/setting.py
+%%PYTHON_SITELIBDIR%%/cogent/recalculation/setting.pyc
+%%PYTHON_SITELIBDIR%%/cogent/recalculation/setting.pyo
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/analysis.py
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/analysis.pyc
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/analysis.pyo
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/birth_death.py
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/birth_death.pyc
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/birth_death.pyo
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/markov.py
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/markov.pyc
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/markov.pyo
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/microarray.py
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/microarray.pyc
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/microarray.pyo
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/microarray_normalize.py
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/microarray_normalize.pyc
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/microarray_normalize.pyo
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/randomization.py
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/randomization.pyc
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/randomization.pyo
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/searchpath.py
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/searchpath.pyc
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/searchpath.pyo
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/sequence_generators.py
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/sequence_generators.pyc
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/sequence_generators.pyo
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/tree.py
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/tree.pyc
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/tree.pyo
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/usage.py
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/usage.pyc
+%%PYTHON_SITELIBDIR%%/cogent/seqsim/usage.pyo
+%%PYTHON_SITELIBDIR%%/cogent/struct/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/struct/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/struct/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/struct/dihedral.py
+%%PYTHON_SITELIBDIR%%/cogent/struct/dihedral.pyc
+%%PYTHON_SITELIBDIR%%/cogent/struct/dihedral.pyo
+%%PYTHON_SITELIBDIR%%/cogent/struct/knots.py
+%%PYTHON_SITELIBDIR%%/cogent/struct/knots.pyc
+%%PYTHON_SITELIBDIR%%/cogent/struct/knots.pyo
+%%PYTHON_SITELIBDIR%%/cogent/struct/pairs_util.py
+%%PYTHON_SITELIBDIR%%/cogent/struct/pairs_util.pyc
+%%PYTHON_SITELIBDIR%%/cogent/struct/pairs_util.pyo
+%%PYTHON_SITELIBDIR%%/cogent/struct/rna2d.py
+%%PYTHON_SITELIBDIR%%/cogent/struct/rna2d.pyc
+%%PYTHON_SITELIBDIR%%/cogent/struct/rna2d.pyo
+%%PYTHON_SITELIBDIR%%/cogent/util/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/util/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/util/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/util/array.py
+%%PYTHON_SITELIBDIR%%/cogent/util/array.pyc
+%%PYTHON_SITELIBDIR%%/cogent/util/array.pyo
+%%PYTHON_SITELIBDIR%%/cogent/util/checkpointing.py
+%%PYTHON_SITELIBDIR%%/cogent/util/checkpointing.pyc
+%%PYTHON_SITELIBDIR%%/cogent/util/checkpointing.pyo
+%%PYTHON_SITELIBDIR%%/cogent/util/datatypes.py
+%%PYTHON_SITELIBDIR%%/cogent/util/datatypes.pyc
+%%PYTHON_SITELIBDIR%%/cogent/util/datatypes.pyo
+%%PYTHON_SITELIBDIR%%/cogent/util/dict2d.py
+%%PYTHON_SITELIBDIR%%/cogent/util/dict2d.pyc
+%%PYTHON_SITELIBDIR%%/cogent/util/dict2d.pyo
+%%PYTHON_SITELIBDIR%%/cogent/util/dict_array.py
+%%PYTHON_SITELIBDIR%%/cogent/util/dict_array.pyc
+%%PYTHON_SITELIBDIR%%/cogent/util/dict_array.pyo
+%%PYTHON_SITELIBDIR%%/cogent/util/misc.py
+%%PYTHON_SITELIBDIR%%/cogent/util/misc.pyc
+%%PYTHON_SITELIBDIR%%/cogent/util/misc.pyo
+%%PYTHON_SITELIBDIR%%/cogent/util/modules.py
+%%PYTHON_SITELIBDIR%%/cogent/util/modules.pyc
+%%PYTHON_SITELIBDIR%%/cogent/util/modules.pyo
+%%PYTHON_SITELIBDIR%%/cogent/util/organizer.py
+%%PYTHON_SITELIBDIR%%/cogent/util/organizer.pyc
+%%PYTHON_SITELIBDIR%%/cogent/util/organizer.pyo
+%%PYTHON_SITELIBDIR%%/cogent/util/parallel.py
+%%PYTHON_SITELIBDIR%%/cogent/util/parallel.pyc
+%%PYTHON_SITELIBDIR%%/cogent/util/parallel.pyo
+%%PYTHON_SITELIBDIR%%/cogent/util/recode_alignment.py
+%%PYTHON_SITELIBDIR%%/cogent/util/recode_alignment.pyc
+%%PYTHON_SITELIBDIR%%/cogent/util/recode_alignment.pyo
+%%PYTHON_SITELIBDIR%%/cogent/util/table.py
+%%PYTHON_SITELIBDIR%%/cogent/util/table.pyc
+%%PYTHON_SITELIBDIR%%/cogent/util/table.pyo
+%%PYTHON_SITELIBDIR%%/cogent/util/transform.py
+%%PYTHON_SITELIBDIR%%/cogent/util/transform.pyc
+%%PYTHON_SITELIBDIR%%/cogent/util/transform.pyo
+%%PYTHON_SITELIBDIR%%/cogent/util/unit_test.py
+%%PYTHON_SITELIBDIR%%/cogent/util/unit_test.pyc
+%%PYTHON_SITELIBDIR%%/cogent/util/unit_test.pyo
+%%PYTHON_SITELIBDIR%%/cogent/util/update_version.py
+%%PYTHON_SITELIBDIR%%/cogent/util/update_version.pyc
+%%PYTHON_SITELIBDIR%%/cogent/util/update_version.pyo
+%%PYTHON_SITELIBDIR%%/cogent/util/warning.py
+%%PYTHON_SITELIBDIR%%/cogent/util/warning.pyc
+%%PYTHON_SITELIBDIR%%/cogent/util/warning.pyo
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/align/weights
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/align
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/app
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/cluster
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/core
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/data
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/db/ensembl
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/db
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/draw/matplotlib
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/draw
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/evolve
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/format
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/maths/matrix
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/maths/stats
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/maths/unifrac
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/maths
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/motif
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/parse
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/phylo
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/recalculation
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/seqsim
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/struct
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/util
+@dirrm %%PYTHON_SITELIBDIR%%/cogent/