3 files changed, 126 insertions, 30 deletions

diff --git a/biology/pycogent/Makefile b/biology/pycogent/Makefile
index f02ab903b8ff..24c75197ebb2 100644
--- a/biology/pycogent/Makefile
+++ b/biology/pycogent/Makefile
@@ -6,13 +6,13 @@
 #
 
 PORTNAME=	pycogent
-PORTVERSION=	1.3.1
+PORTVERSION=	1.4
 CATEGORIES=	biology python
 MASTER_SITES=	SF/${PORTNAME}/PyCogent/${PORTVERSION}
 DISTNAME=	PyCogent-${PORTVERSION}
 EXTRACT_SUFX=	.tgz
 
-MAINTAINER=	wenheping@gmail.com
+MAINTAINER=	wen@FreeBSD.org
 COMMENT=	A toolkit for statistical analysis of biological sequences
 
 BUILD_DEPENDS=	${PYNUMPY} \
diff --git a/biology/pycogent/distinfo b/biology/pycogent/distinfo
index 09398220a025..7d83df192558 100644
--- a/biology/pycogent/distinfo
+++ b/biology/pycogent/distinfo
@@ -1,3 +1,3 @@
-MD5 (PyCogent-1.3.1.tgz) = 4cc108a69e5ffd343508db4615514b74
-SHA256 (PyCogent-1.3.1.tgz) = 56636a2aeee464968056458f8384262f874cdac12b89a43c4c3e5d88582a7fc6
-SIZE (PyCogent-1.3.1.tgz) = 2062874
+MD5 (PyCogent-1.4.tgz) = 3d28963a7c5ba6dc615fb985cb7e3655
+SHA256 (PyCogent-1.4.tgz) = b02554fcd60b101d7f8a2fe147cf5c2c4084a5ba6623bad59cf69b088219136b
+SIZE (PyCogent-1.4.tgz) = 5125606
diff --git a/biology/pycogent/pkg-plist b/biology/pycogent/pkg-plist
index a1bc29f1f35d..da00c54e6eb3 100644
--- a/biology/pycogent/pkg-plist
+++ b/biology/pycogent/pkg-plist
@@ -97,6 +97,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/app/foldalign.py
 %%PYTHON_SITELIBDIR%%/cogent/app/foldalign.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/foldalign.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/formatdb.py
+%%PYTHON_SITELIBDIR%%/cogent/app/formatdb.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/formatdb.pyo
 %%PYTHON_SITELIBDIR%%/cogent/app/gctmpca.py
 %%PYTHON_SITELIBDIR%%/cogent/app/gctmpca.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/gctmpca.pyo
@@ -109,15 +112,15 @@
 %%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/mothur.py
+%%PYTHON_SITELIBDIR%%/cogent/app/mothur.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/mothur.pyo
 %%PYTHON_SITELIBDIR%%/cogent/app/muscle.py
 %%PYTHON_SITELIBDIR%%/cogent/app/muscle.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/muscle.pyo
@@ -136,6 +139,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/app/raxml.py
 %%PYTHON_SITELIBDIR%%/cogent/app/raxml.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/raxml.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/rdp_classifier.py
+%%PYTHON_SITELIBDIR%%/cogent/app/rdp_classifier.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/rdp_classifier.pyo
 %%PYTHON_SITELIBDIR%%/cogent/app/rnaalifold.py
 %%PYTHON_SITELIBDIR%%/cogent/app/rnaalifold.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/rnaalifold.pyo
@@ -151,6 +157,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/app/sfold.py
 %%PYTHON_SITELIBDIR%%/cogent/app/sfold.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/sfold.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/stride.py
+%%PYTHON_SITELIBDIR%%/cogent/app/stride.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/stride.pyo
 %%PYTHON_SITELIBDIR%%/cogent/app/unafold.py
 %%PYTHON_SITELIBDIR%%/cogent/app/unafold.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/unafold.pyo
@@ -166,12 +175,18 @@
 %%PYTHON_SITELIBDIR%%/cogent/cluster/__init__.py
 %%PYTHON_SITELIBDIR%%/cogent/cluster/__init__.pyc
 %%PYTHON_SITELIBDIR%%/cogent/cluster/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/cluster/goodness_of_fit.py
+%%PYTHON_SITELIBDIR%%/cogent/cluster/goodness_of_fit.pyc
+%%PYTHON_SITELIBDIR%%/cogent/cluster/goodness_of_fit.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/cluster/procrustes.py
+%%PYTHON_SITELIBDIR%%/cogent/cluster/procrustes.pyc
+%%PYTHON_SITELIBDIR%%/cogent/cluster/procrustes.pyo
 %%PYTHON_SITELIBDIR%%/cogent/core/__init__.py
 %%PYTHON_SITELIBDIR%%/cogent/core/__init__.pyc
 %%PYTHON_SITELIBDIR%%/cogent/core/__init__.pyo
@@ -187,6 +202,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/core/bitvector.py
 %%PYTHON_SITELIBDIR%%/cogent/core/bitvector.pyc
 %%PYTHON_SITELIBDIR%%/cogent/core/bitvector.pyo
+%%PYTHON_SITELIBDIR%%/cogent/core/entity.py
+%%PYTHON_SITELIBDIR%%/cogent/core/entity.pyc
+%%PYTHON_SITELIBDIR%%/cogent/core/entity.pyo
 %%PYTHON_SITELIBDIR%%/cogent/core/genetic_code.py
 %%PYTHON_SITELIBDIR%%/cogent/core/genetic_code.pyc
 %%PYTHON_SITELIBDIR%%/cogent/core/genetic_code.pyo
@@ -217,9 +235,18 @@
 %%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/ligand_properties.py
+%%PYTHON_SITELIBDIR%%/cogent/data/ligand_properties.pyc
+%%PYTHON_SITELIBDIR%%/cogent/data/ligand_properties.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/data/nucleic_properties.py
+%%PYTHON_SITELIBDIR%%/cogent/data/nucleic_properties.pyc
+%%PYTHON_SITELIBDIR%%/cogent/data/nucleic_properties.pyo
+%%PYTHON_SITELIBDIR%%/cogent/data/protein_properties.py
+%%PYTHON_SITELIBDIR%%/cogent/data/protein_properties.pyc
+%%PYTHON_SITELIBDIR%%/cogent/data/protein_properties.pyo
 %%PYTHON_SITELIBDIR%%/cogent/db/__init__.py
 %%PYTHON_SITELIBDIR%%/cogent/db/__init__.pyc
 %%PYTHON_SITELIBDIR%%/cogent/db/__init__.pyo
@@ -277,39 +304,39 @@
 %%PYTHON_SITELIBDIR%%/cogent/draw/__init__.py
 %%PYTHON_SITELIBDIR%%/cogent/draw/__init__.pyc
 %%PYTHON_SITELIBDIR%%/cogent/draw/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/draw/arrow_rates.py
+%%PYTHON_SITELIBDIR%%/cogent/draw/arrow_rates.pyc
+%%PYTHON_SITELIBDIR%%/cogent/draw/arrow_rates.pyo
+%%PYTHON_SITELIBDIR%%/cogent/draw/codon_usage.py
+%%PYTHON_SITELIBDIR%%/cogent/draw/codon_usage.pyc
+%%PYTHON_SITELIBDIR%%/cogent/draw/codon_usage.pyo
 %%PYTHON_SITELIBDIR%%/cogent/draw/dendrogram.py
 %%PYTHON_SITELIBDIR%%/cogent/draw/dendrogram.pyc
 %%PYTHON_SITELIBDIR%%/cogent/draw/dendrogram.pyo
+%%PYTHON_SITELIBDIR%%/cogent/draw/dinuc.py
+%%PYTHON_SITELIBDIR%%/cogent/draw/dinuc.pyc
+%%PYTHON_SITELIBDIR%%/cogent/draw/dinuc.pyo
 %%PYTHON_SITELIBDIR%%/cogent/draw/dotplot.py
 %%PYTHON_SITELIBDIR%%/cogent/draw/dotplot.pyc
 %%PYTHON_SITELIBDIR%%/cogent/draw/dotplot.pyo
+%%PYTHON_SITELIBDIR%%/cogent/draw/fancy_arrow.py
+%%PYTHON_SITELIBDIR%%/cogent/draw/fancy_arrow.pyc
+%%PYTHON_SITELIBDIR%%/cogent/draw/fancy_arrow.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/draw/multivariate_plot.py
+%%PYTHON_SITELIBDIR%%/cogent/draw/multivariate_plot.pyc
+%%PYTHON_SITELIBDIR%%/cogent/draw/multivariate_plot.pyo
+%%PYTHON_SITELIBDIR%%/cogent/draw/rlg2mpl.py
+%%PYTHON_SITELIBDIR%%/cogent/draw/rlg2mpl.pyc
+%%PYTHON_SITELIBDIR%%/cogent/draw/rlg2mpl.pyo
+%%PYTHON_SITELIBDIR%%/cogent/draw/util.py
+%%PYTHON_SITELIBDIR%%/cogent/draw/util.pyc
+%%PYTHON_SITELIBDIR%%/cogent/draw/util.pyo
 %%PYTHON_SITELIBDIR%%/cogent/evolve/__init__.py
 %%PYTHON_SITELIBDIR%%/cogent/evolve/__init__.pyc
 %%PYTHON_SITELIBDIR%%/cogent/evolve/__init__.pyo
@@ -335,6 +362,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/evolve/models.py
 %%PYTHON_SITELIBDIR%%/cogent/evolve/models.pyc
 %%PYTHON_SITELIBDIR%%/cogent/evolve/models.pyo
+%%PYTHON_SITELIBDIR%%/cogent/evolve/motif_prob_model.py
+%%PYTHON_SITELIBDIR%%/cogent/evolve/motif_prob_model.pyc
+%%PYTHON_SITELIBDIR%%/cogent/evolve/motif_prob_model.pyo
 %%PYTHON_SITELIBDIR%%/cogent/evolve/parameter_controller.py
 %%PYTHON_SITELIBDIR%%/cogent/evolve/parameter_controller.pyc
 %%PYTHON_SITELIBDIR%%/cogent/evolve/parameter_controller.pyo
@@ -371,6 +401,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/format/nexus.py
 %%PYTHON_SITELIBDIR%%/cogent/format/nexus.pyc
 %%PYTHON_SITELIBDIR%%/cogent/format/nexus.pyo
+%%PYTHON_SITELIBDIR%%/cogent/format/pdb.py
+%%PYTHON_SITELIBDIR%%/cogent/format/pdb.pyc
+%%PYTHON_SITELIBDIR%%/cogent/format/pdb.pyo
 %%PYTHON_SITELIBDIR%%/cogent/format/pdb_color.py
 %%PYTHON_SITELIBDIR%%/cogent/format/pdb_color.pyc
 %%PYTHON_SITELIBDIR%%/cogent/format/pdb_color.pyo
@@ -383,12 +416,18 @@
 %%PYTHON_SITELIBDIR%%/cogent/format/stockholm.py
 %%PYTHON_SITELIBDIR%%/cogent/format/stockholm.pyc
 %%PYTHON_SITELIBDIR%%/cogent/format/stockholm.pyo
+%%PYTHON_SITELIBDIR%%/cogent/format/structure.py
+%%PYTHON_SITELIBDIR%%/cogent/format/structure.pyc
+%%PYTHON_SITELIBDIR%%/cogent/format/structure.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/format/xyzrn.py
+%%PYTHON_SITELIBDIR%%/cogent/format/xyzrn.pyc
+%%PYTHON_SITELIBDIR%%/cogent/format/xyzrn.pyo
 %%PYTHON_SITELIBDIR%%/cogent/maths/__init__.py
 %%PYTHON_SITELIBDIR%%/cogent/maths/__init__.pyc
 %%PYTHON_SITELIBDIR%%/cogent/maths/__init__.pyo
@@ -435,9 +474,16 @@
 %%PYTHON_SITELIBDIR%%/cogent/maths/solve.py
 %%PYTHON_SITELIBDIR%%/cogent/maths/solve.pyc
 %%PYTHON_SITELIBDIR%%/cogent/maths/solve.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/spatial/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/spatial/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/spatial/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/spatial/ckd3.so
 %%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/alpha_diversity.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/alpha_diversity.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/alpha_diversity.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
@@ -465,6 +511,9 @@
 %%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/rarefaction.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/rarefaction.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/rarefaction.pyo
 %%PYTHON_SITELIBDIR%%/cogent/maths/stats/test.py
 %%PYTHON_SITELIBDIR%%/cogent/maths/stats/test.pyc
 %%PYTHON_SITELIBDIR%%/cogent/maths/stats/test.pyo
@@ -504,6 +553,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/parse/blast.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/blast.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/blast.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/blast_xml.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/blast_xml.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/blast_xml.pyo
 %%PYTHON_SITELIBDIR%%/cogent/parse/bpseq.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/bpseq.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/bpseq.pyo
@@ -576,6 +628,15 @@
 %%PYTHON_SITELIBDIR%%/cogent/parse/gibbs.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/gibbs.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/gibbs.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/flowgram.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/flowgram.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/flowgram.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/flowgram_collection.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/flowgram_collection.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/flowgram_collection.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/flowgram_parser.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/flowgram_parser.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/flowgram_parser.pyo
 %%PYTHON_SITELIBDIR%%/cogent/parse/ilm.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/ilm.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/ilm.pyo
@@ -600,6 +661,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/parse/mfold.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/mfold.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/mfold.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/mothur.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/mothur.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/mothur.pyo
 %%PYTHON_SITELIBDIR%%/cogent/parse/ncbi_taxonomy.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/ncbi_taxonomy.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/ncbi_taxonomy.pyo
@@ -618,6 +682,9 @@
 %%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/pdb.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/pdb.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/pdb.pyo
 %%PYTHON_SITELIBDIR%%/cogent/parse/pfold.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/pfold.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/pfold.pyo
@@ -666,6 +733,12 @@
 %%PYTHON_SITELIBDIR%%/cogent/parse/sprinzl.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/sprinzl.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/sprinzl.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/stride.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/stride.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/stride.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/structure.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/structure.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/structure.pyo
 %%PYTHON_SITELIBDIR%%/cogent/parse/table.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/table.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/table.pyo
@@ -687,6 +760,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/phylo/__init__.py
 %%PYTHON_SITELIBDIR%%/cogent/phylo/__init__.pyc
 %%PYTHON_SITELIBDIR%%/cogent/phylo/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/phylo/compatibility.py
+%%PYTHON_SITELIBDIR%%/cogent/phylo/compatibility.pyc
+%%PYTHON_SITELIBDIR%%/cogent/phylo/compatibility.pyo
 %%PYTHON_SITELIBDIR%%/cogent/phylo/consensus.py
 %%PYTHON_SITELIBDIR%%/cogent/phylo/consensus.pyc
 %%PYTHON_SITELIBDIR%%/cogent/phylo/consensus.pyo
@@ -756,21 +832,38 @@
 %%PYTHON_SITELIBDIR%%/cogent/seqsim/usage.py
 %%PYTHON_SITELIBDIR%%/cogent/seqsim/usage.pyc
 %%PYTHON_SITELIBDIR%%/cogent/seqsim/usage.pyo
+%%PYTHON_SITELIBDIR%%/cogent/struct/_asa.so
+%%PYTHON_SITELIBDIR%%/cogent/struct/_contact.so
 %%PYTHON_SITELIBDIR%%/cogent/struct/__init__.py
 %%PYTHON_SITELIBDIR%%/cogent/struct/__init__.pyc
 %%PYTHON_SITELIBDIR%%/cogent/struct/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/struct/annotation.py
+%%PYTHON_SITELIBDIR%%/cogent/struct/annotation.pyc
+%%PYTHON_SITELIBDIR%%/cogent/struct/annotation.pyo
+%%PYTHON_SITELIBDIR%%/cogent/struct/asa.py
+%%PYTHON_SITELIBDIR%%/cogent/struct/asa.pyc
+%%PYTHON_SITELIBDIR%%/cogent/struct/asa.pyo
+%%PYTHON_SITELIBDIR%%/cogent/struct/contact.py
+%%PYTHON_SITELIBDIR%%/cogent/struct/contact.pyc
+%%PYTHON_SITELIBDIR%%/cogent/struct/contact.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/manipulation.py
+%%PYTHON_SITELIBDIR%%/cogent/struct/manipulation.pyc
+%%PYTHON_SITELIBDIR%%/cogent/struct/manipulation.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/struct/selection.py
+%%PYTHON_SITELIBDIR%%/cogent/struct/selection.pyc
+%%PYTHON_SITELIBDIR%%/cogent/struct/selection.pyo
 %%PYTHON_SITELIBDIR%%/cogent/util/__init__.py
 %%PYTHON_SITELIBDIR%%/cogent/util/__init__.pyc
 %%PYTHON_SITELIBDIR%%/cogent/util/__init__.pyo
@@ -810,6 +903,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/util/transform.py
 %%PYTHON_SITELIBDIR%%/cogent/util/transform.pyc
 %%PYTHON_SITELIBDIR%%/cogent/util/transform.pyo
+%%PYTHON_SITELIBDIR%%/cogent/util/trie.py
+%%PYTHON_SITELIBDIR%%/cogent/util/trie.pyc
+%%PYTHON_SITELIBDIR%%/cogent/util/trie.pyo
 %%PYTHON_SITELIBDIR%%/cogent/util/unit_test.py
 %%PYTHON_SITELIBDIR%%/cogent/util/unit_test.pyc
 %%PYTHON_SITELIBDIR%%/cogent/util/unit_test.pyo
@@ -827,11 +923,11 @@
 @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/spatial
 @dirrm %%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai
 @dirrm %%PYTHON_SITELIBDIR%%/cogent/maths/stats
 @dirrm %%PYTHON_SITELIBDIR%%/cogent/maths/unifrac