3 files changed, 25 insertions, 4 deletions

diff --git a/biology/pycogent/Makefile b/biology/pycogent/Makefile
index 24c75197ebb2..12c45ec638fc 100644
--- a/biology/pycogent/Makefile
+++ b/biology/pycogent/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	pycogent
-PORTVERSION=	1.4
+PORTVERSION=	1.4.1
 CATEGORIES=	biology python
 MASTER_SITES=	SF/${PORTNAME}/PyCogent/${PORTVERSION}
 DISTNAME=	PyCogent-${PORTVERSION}
diff --git a/biology/pycogent/distinfo b/biology/pycogent/distinfo
index 7d83df192558..b2b07ecb99f3 100644
--- a/biology/pycogent/distinfo
+++ b/biology/pycogent/distinfo
@@ -1,3 +1,3 @@
-MD5 (PyCogent-1.4.tgz) = 3d28963a7c5ba6dc615fb985cb7e3655
-SHA256 (PyCogent-1.4.tgz) = b02554fcd60b101d7f8a2fe147cf5c2c4084a5ba6623bad59cf69b088219136b
-SIZE (PyCogent-1.4.tgz) = 5125606
+MD5 (PyCogent-1.4.1.tgz) = c5f50b108d87001d0840a7f721f78977
+SHA256 (PyCogent-1.4.1.tgz) = 4f0275c7b97e22b8a8286e8c5831599871f66bcf6bbb8f2dd70d3e300df3a217
+SIZE (PyCogent-1.4.1.tgz) = 2596901
diff --git a/biology/pycogent/pkg-plist b/biology/pycogent/pkg-plist
index da00c54e6eb3..d29214841cae 100644
--- a/biology/pycogent/pkg-plist
+++ b/biology/pycogent/pkg-plist
@@ -121,6 +121,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/app/mothur.py
 %%PYTHON_SITELIBDIR%%/cogent/app/mothur.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/mothur.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/msms.py
+%%PYTHON_SITELIBDIR%%/cogent/app/msms.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/msms.pyo
 %%PYTHON_SITELIBDIR%%/cogent/app/muscle.py
 %%PYTHON_SITELIBDIR%%/cogent/app/muscle.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/muscle.pyo
@@ -154,12 +157,21 @@
 %%PYTHON_SITELIBDIR%%/cogent/app/rnaview.py
 %%PYTHON_SITELIBDIR%%/cogent/app/rnaview.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/rnaview.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/sfffile.py
+%%PYTHON_SITELIBDIR%%/cogent/app/sfffile.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/sfffile.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/sffinfo.py
+%%PYTHON_SITELIBDIR%%/cogent/app/sffinfo.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/sffinfo.pyo
 %%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/uclust.py
+%%PYTHON_SITELIBDIR%%/cogent/app/uclust.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/uclust.pyo
 %%PYTHON_SITELIBDIR%%/cogent/app/unafold.py
 %%PYTHON_SITELIBDIR%%/cogent/app/unafold.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/unafold.pyo
@@ -350,6 +362,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/evolve/coevolution.py
 %%PYTHON_SITELIBDIR%%/cogent/evolve/coevolution.pyc
 %%PYTHON_SITELIBDIR%%/cogent/evolve/coevolution.pyo
+%%PYTHON_SITELIBDIR%%/cogent/evolve/discrete_markov.py
+%%PYTHON_SITELIBDIR%%/cogent/evolve/discrete_markov.pyc
+%%PYTHON_SITELIBDIR%%/cogent/evolve/discrete_markov.pyo
 %%PYTHON_SITELIBDIR%%/cogent/evolve/likelihood_calculation.py
 %%PYTHON_SITELIBDIR%%/cogent/evolve/likelihood_calculation.pyc
 %%PYTHON_SITELIBDIR%%/cogent/evolve/likelihood_calculation.pyo
@@ -664,6 +679,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/parse/mothur.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/mothur.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/mothur.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/msms.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/msms.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/msms.pyo
 %%PYTHON_SITELIBDIR%%/cogent/parse/ncbi_taxonomy.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/ncbi_taxonomy.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/ncbi_taxonomy.pyo
@@ -778,6 +796,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/phylo/nj.py
 %%PYTHON_SITELIBDIR%%/cogent/phylo/nj.pyc
 %%PYTHON_SITELIBDIR%%/cogent/phylo/nj.pyo
+%%PYTHON_SITELIBDIR%%/cogent/phylo/tree_collection.py
+%%PYTHON_SITELIBDIR%%/cogent/phylo/tree_collection.pyc
+%%PYTHON_SITELIBDIR%%/cogent/phylo/tree_collection.pyo
 %%PYTHON_SITELIBDIR%%/cogent/phylo/tree_space.py
 %%PYTHON_SITELIBDIR%%/cogent/phylo/tree_space.pyc
 %%PYTHON_SITELIBDIR%%/cogent/phylo/tree_space.pyo