3 files changed, 18 insertions, 111 deletions

diff --git a/biology/py-biopython/Makefile b/biology/py-biopython/Makefile
index 8579da33ec5..a08c1eebc8e 100644
--- a/biology/py-biopython/Makefile
+++ b/biology/py-biopython/Makefile
@@ -6,8 +6,7 @@
 #
 
 PORTNAME=	biopython
-PORTVERSION=	1.54
-PORTREVISION=	1
+PORTVERSION=	1.57
 CATEGORIES=	biology python
 MASTER_SITES=	http://www.biopython.org/DIST/
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
diff --git a/biology/py-biopython/distinfo b/biology/py-biopython/distinfo
index a25f15b0cf8..0e12b09b232 100644
--- a/biology/py-biopython/distinfo
+++ b/biology/py-biopython/distinfo
@@ -1,2 +1,2 @@
-SHA256 (biopython-1.54.tar.gz) = 6f704698d68af75b3601b2a862386682b2317038b8bbaf2eb2ad68c1e1a4dc35
-SIZE (biopython-1.54.tar.gz) = 6445527
+SHA256 (biopython-1.57.tar.gz) = 07c16a86127770c8d5b653a6e82fee0999159f7284a3a01c98cf66ed2f0ec4a0
+SIZE (biopython-1.57.tar.gz) = 6945024
diff --git a/biology/py-biopython/pkg-plist b/biology/py-biopython/pkg-plist
index afc36f56349..d28ea882ada 100644
--- a/biology/py-biopython/pkg-plist
+++ b/biology/py-biopython/pkg-plist
@@ -1,3 +1,6 @@
+%%PYTHON_SITELIBDIR%%/Bio/_py3k.py
+%%PYTHON_SITELIBDIR%%/Bio/_py3k.pyc
+%%PYTHON_SITELIBDIR%%/Bio/_py3k.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Affy/CelFile.py
 %%PYTHON_SITELIBDIR%%/Bio/Affy/CelFile.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Affy/CelFile.pyo
@@ -31,36 +34,12 @@
 %%PYTHON_SITELIBDIR%%/Bio/Align/Applications/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/Align/Applications/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Align/Applications/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Align/FormatConvert.py
-%%PYTHON_SITELIBDIR%%/Bio/Align/FormatConvert.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Align/FormatConvert.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Align/Generic.py
 %%PYTHON_SITELIBDIR%%/Bio/Align/Generic.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Align/Generic.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Align/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/Align/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Align/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/AlignAce/AlignAceStandalone.py
-%%PYTHON_SITELIBDIR%%/Bio/AlignAce/AlignAceStandalone.pyc
-%%PYTHON_SITELIBDIR%%/Bio/AlignAce/AlignAceStandalone.pyo
-%%PYTHON_SITELIBDIR%%/Bio/AlignAce/Applications.py
-%%PYTHON_SITELIBDIR%%/Bio/AlignAce/Applications.pyc
-%%PYTHON_SITELIBDIR%%/Bio/AlignAce/Applications.pyo
-%%PYTHON_SITELIBDIR%%/Bio/AlignAce/CompareAceStandalone.py
-%%PYTHON_SITELIBDIR%%/Bio/AlignAce/CompareAceStandalone.pyc
-%%PYTHON_SITELIBDIR%%/Bio/AlignAce/CompareAceStandalone.pyo
-%%PYTHON_SITELIBDIR%%/Bio/AlignAce/Motif.py
-%%PYTHON_SITELIBDIR%%/Bio/AlignAce/Motif.pyc
-%%PYTHON_SITELIBDIR%%/Bio/AlignAce/Motif.pyo
-%%PYTHON_SITELIBDIR%%/Bio/AlignAce/Parser.py
-%%PYTHON_SITELIBDIR%%/Bio/AlignAce/Parser.pyc
-%%PYTHON_SITELIBDIR%%/Bio/AlignAce/Parser.pyo
-%%PYTHON_SITELIBDIR%%/Bio/AlignAce/Scanner.py
-%%PYTHON_SITELIBDIR%%/Bio/AlignAce/Scanner.pyc
-%%PYTHON_SITELIBDIR%%/Bio/AlignAce/Scanner.pyo
-%%PYTHON_SITELIBDIR%%/Bio/AlignAce/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/AlignAce/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/AlignAce/__init__.pyo
 %%PYTHON_SITELIBDIR%%/Bio/AlignIO/ClustalIO.py
 %%PYTHON_SITELIBDIR%%/Bio/AlignIO/ClustalIO.pyc
 %%PYTHON_SITELIBDIR%%/Bio/AlignIO/ClustalIO.pyo
@@ -146,9 +125,6 @@
 %%PYTHON_SITELIBDIR%%/Bio/DocSQL.py
 %%PYTHON_SITELIBDIR%%/Bio/DocSQL.pyc
 %%PYTHON_SITELIBDIR%%/Bio/DocSQL.pyo
-%%PYTHON_SITELIBDIR%%/Bio/EZRetrieve.py
-%%PYTHON_SITELIBDIR%%/Bio/EZRetrieve.pyc
-%%PYTHON_SITELIBDIR%%/Bio/EZRetrieve.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/Applications.py
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/Applications.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/Applications.pyo
@@ -161,12 +137,6 @@
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Encodings/IUPACEncoding.py
-%%PYTHON_SITELIBDIR%%/Bio/Encodings/IUPACEncoding.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Encodings/IUPACEncoding.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Encodings/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/Encodings/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Encodings/__init__.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/EMBL_General.mod.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/GenBank_General.mod.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/HomoloGene.dtd
@@ -213,6 +183,7 @@
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/archivecustom-modules.ent
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/articlemeta.ent
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/backmatter.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/bookdoc_100301.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/chars.ent
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/common.ent
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/default-classes.ent
@@ -272,7 +243,10 @@
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmserials_080101.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmserials_100101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/notat.ent
@@ -283,6 +257,8 @@
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pubmed_080101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pubmed_090101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pubmed_100101.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pubmed_100301.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pubmed_110101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/references.ent
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/section.ent
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/taxon.dtd
@@ -293,9 +269,6 @@
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Enzyme/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/Enzyme/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Enzyme/__init__.pyo
 %%PYTHON_SITELIBDIR%%/Bio/ExPASy/Enzyme.py
 %%PYTHON_SITELIBDIR%%/Bio/ExPASy/Enzyme.pyc
 %%PYTHON_SITELIBDIR%%/Bio/ExPASy/Enzyme.pyo
@@ -320,18 +293,9 @@
 %%PYTHON_SITELIBDIR%%/Bio/FSSP/fssp_rec.py
 %%PYTHON_SITELIBDIR%%/Bio/FSSP/fssp_rec.pyc
 %%PYTHON_SITELIBDIR%%/Bio/FSSP/fssp_rec.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Fasta/FastaAlign.py
-%%PYTHON_SITELIBDIR%%/Bio/Fasta/FastaAlign.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Fasta/FastaAlign.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Fasta/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/Fasta/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Fasta/__init__.pyo
 %%PYTHON_SITELIBDIR%%/Bio/File.py
 %%PYTHON_SITELIBDIR%%/Bio/File.pyc
 %%PYTHON_SITELIBDIR%%/Bio/File.pyo
-%%PYTHON_SITELIBDIR%%/Bio/FilteredReader.py
-%%PYTHON_SITELIBDIR%%/Bio/FilteredReader.pyc
-%%PYTHON_SITELIBDIR%%/Bio/FilteredReader.pyo
 %%PYTHON_SITELIBDIR%%/Bio/GA/Crossover/General.py
 %%PYTHON_SITELIBDIR%%/Bio/GA/Crossover/General.pyc
 %%PYTHON_SITELIBDIR%%/Bio/GA/Crossover/General.pyo
@@ -389,18 +353,6 @@
 %%PYTHON_SITELIBDIR%%/Bio/GA/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/GA/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/GA/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/GFF/GenericTools.py
-%%PYTHON_SITELIBDIR%%/Bio/GFF/GenericTools.pyc
-%%PYTHON_SITELIBDIR%%/Bio/GFF/GenericTools.pyo
-%%PYTHON_SITELIBDIR%%/Bio/GFF/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/GFF/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/GFF/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/GFF/binning.py
-%%PYTHON_SITELIBDIR%%/Bio/GFF/binning.pyc
-%%PYTHON_SITELIBDIR%%/Bio/GFF/binning.pyo
-%%PYTHON_SITELIBDIR%%/Bio/GFF/easy.py
-%%PYTHON_SITELIBDIR%%/Bio/GFF/easy.pyc
-%%PYTHON_SITELIBDIR%%/Bio/GFF/easy.pyo
 %%PYTHON_SITELIBDIR%%/Bio/GenBank/LocationParser.py
 %%PYTHON_SITELIBDIR%%/Bio/GenBank/LocationParser.pyc
 %%PYTHON_SITELIBDIR%%/Bio/GenBank/LocationParser.pyo
@@ -516,15 +468,6 @@
 %%PYTHON_SITELIBDIR%%/Bio/LogisticRegression.py
 %%PYTHON_SITELIBDIR%%/Bio/LogisticRegression.pyc
 %%PYTHON_SITELIBDIR%%/Bio/LogisticRegression.pyo
-%%PYTHON_SITELIBDIR%%/Bio/MEME/Motif.py
-%%PYTHON_SITELIBDIR%%/Bio/MEME/Motif.pyc
-%%PYTHON_SITELIBDIR%%/Bio/MEME/Motif.pyo
-%%PYTHON_SITELIBDIR%%/Bio/MEME/Parser.py
-%%PYTHON_SITELIBDIR%%/Bio/MEME/Parser.pyc
-%%PYTHON_SITELIBDIR%%/Bio/MEME/Parser.pyo
-%%PYTHON_SITELIBDIR%%/Bio/MEME/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/MEME/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/MEME/__init__.pyo
 %%PYTHON_SITELIBDIR%%/Bio/MarkovModel.py
 %%PYTHON_SITELIBDIR%%/Bio/MarkovModel.pyc
 %%PYTHON_SITELIBDIR%%/Bio/MarkovModel.pyo
@@ -574,9 +517,6 @@
 %%PYTHON_SITELIBDIR%%/Bio/NaiveBayes.py
 %%PYTHON_SITELIBDIR%%/Bio/NaiveBayes.pyc
 %%PYTHON_SITELIBDIR%%/Bio/NaiveBayes.pyo
-%%PYTHON_SITELIBDIR%%/Bio/NetCatch.py
-%%PYTHON_SITELIBDIR%%/Bio/NetCatch.pyc
-%%PYTHON_SITELIBDIR%%/Bio/NetCatch.pyo
 %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork/BackPropagation/Layer.py
 %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork/BackPropagation/Layer.pyc
 %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork/BackPropagation/Layer.pyo
@@ -794,6 +734,9 @@
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/FileParser.py
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/FileParser.pyc
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/FileParser.pyo
+%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/LargeFileParser.py
+%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/LargeFileParser.pyc
+%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/LargeFileParser.pyo
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.py
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.pyc
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.pyo
@@ -828,21 +771,6 @@
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/PropertyManager.py
-%%PYTHON_SITELIBDIR%%/Bio/PropertyManager.pyc
-%%PYTHON_SITELIBDIR%%/Bio/PropertyManager.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Prosite/Pattern.py
-%%PYTHON_SITELIBDIR%%/Bio/Prosite/Pattern.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Prosite/Pattern.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Prosite/Prodoc.py
-%%PYTHON_SITELIBDIR%%/Bio/Prosite/Prodoc.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Prosite/Prodoc.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Prosite/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/Prosite/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Prosite/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Restriction/DNAUtils.py
-%%PYTHON_SITELIBDIR%%/Bio/Restriction/DNAUtils.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Restriction/DNAUtils.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Restriction/PrintFormat.py
 %%PYTHON_SITELIBDIR%%/Bio/Restriction/PrintFormat.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Restriction/PrintFormat.pyo
@@ -936,6 +864,9 @@
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/TabIO.py
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/TabIO.pyc
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/TabIO.pyo
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/UniprotIO.py
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/UniprotIO.pyc
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/UniprotIO.pyo
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/__init__.pyo
@@ -1008,18 +939,9 @@
 %%PYTHON_SITELIBDIR%%/Bio/SwissProt/KeyWList.py
 %%PYTHON_SITELIBDIR%%/Bio/SwissProt/KeyWList.pyc
 %%PYTHON_SITELIBDIR%%/Bio/SwissProt/KeyWList.pyo
-%%PYTHON_SITELIBDIR%%/Bio/SwissProt/SProt.py
-%%PYTHON_SITELIBDIR%%/Bio/SwissProt/SProt.pyc
-%%PYTHON_SITELIBDIR%%/Bio/SwissProt/SProt.pyo
 %%PYTHON_SITELIBDIR%%/Bio/SwissProt/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/SwissProt/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/SwissProt/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Transcribe.py
-%%PYTHON_SITELIBDIR%%/Bio/Transcribe.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Transcribe.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Translate.py
-%%PYTHON_SITELIBDIR%%/Bio/Translate.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Translate.pyo
 %%PYTHON_SITELIBDIR%%/Bio/UniGene/UniGene.py
 %%PYTHON_SITELIBDIR%%/Bio/UniGene/UniGene.pyc
 %%PYTHON_SITELIBDIR%%/Bio/UniGene/UniGene.pyo
@@ -1038,30 +960,17 @@
 %%PYTHON_SITELIBDIR%%/Bio/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/cMarkovModel.so
 %%PYTHON_SITELIBDIR%%/Bio/cpairwise2.so
 %%PYTHON_SITELIBDIR%%/Bio/kNN.py
 %%PYTHON_SITELIBDIR%%/Bio/kNN.pyc
 %%PYTHON_SITELIBDIR%%/Bio/kNN.pyo
-%%PYTHON_SITELIBDIR%%/Bio/listfns.py
-%%PYTHON_SITELIBDIR%%/Bio/listfns.pyc
-%%PYTHON_SITELIBDIR%%/Bio/listfns.pyo
-%%PYTHON_SITELIBDIR%%/Bio/mathfns.py
-%%PYTHON_SITELIBDIR%%/Bio/mathfns.pyc
-%%PYTHON_SITELIBDIR%%/Bio/mathfns.pyo
 %%PYTHON_SITELIBDIR%%/Bio/pairwise2.py
 %%PYTHON_SITELIBDIR%%/Bio/pairwise2.pyc
 %%PYTHON_SITELIBDIR%%/Bio/pairwise2.pyo
-%%PYTHON_SITELIBDIR%%/Bio/stringfns.py
-%%PYTHON_SITELIBDIR%%/Bio/stringfns.pyc
-%%PYTHON_SITELIBDIR%%/Bio/stringfns.pyo
 %%PYTHON_SITELIBDIR%%/Bio/trie.so
 %%PYTHON_SITELIBDIR%%/Bio/triefind.py
 %%PYTHON_SITELIBDIR%%/Bio/triefind.pyc
 %%PYTHON_SITELIBDIR%%/Bio/triefind.pyo
-%%PYTHON_SITELIBDIR%%/Bio/utils.py
-%%PYTHON_SITELIBDIR%%/Bio/utils.pyc
-%%PYTHON_SITELIBDIR%%/Bio/utils.pyo
 %%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.py
 %%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.pyc
 %%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.pyo
@@ -1080,7 +989,6 @@
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Affy
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Align/Applications
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Align
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/AlignAce
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/AlignIO
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Alphabet
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Application