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Abi
Ace
Affy
BWA
BioSQL
Blast
Blat
CDAO
Clustalw
CodonUsage Removing Mac OS hidden meta data file
Compass
EMBL
Emboss Test case where eprimer3 reports oligo without sequence
Entrez Make sure all Entrez tests pass
Enzymes
Exonerate Update exonerate parser to handle dna2protein model
ExtendedPhylip Update tests for extended phylip format
FSSP
Fasta
GFF
GenBank
Geo Updating the input files Tests/geo/soft_ex_*.txt; adding soft_ex_affy…
Graphics
Hmmer
IntelliGenetics
KEGG
MEME
Medline
MetaTool
Motif
NBRF
NeXML
NeuralNetwork Stop annoying cvs update messages for files that are not kept in repo…
Nexus
PAML add test cases for bad codeml tree parsing
PDB
Phd Adding 454 and Solexa derived PHD files from the Consed author David …
Phylip
PhyloXML Phylo: make str(Tree) work with funky unicode chars on Py2/3
PopGen
Prosite
Quality
Rebase
Registry
Roche
SCOP
Saf
SamBam
SeqXML Forgot to add SeqXML file from Thomas
Stockholm
SubsMat
SwissProt SwissProt/UniProt example with semi-colon in gene name
TreeConstruction
UniGene
Wise
codonalign
motifs
output
.cvsignore
common_BioSQL.py
requires_internet.py
requires_wise.py
run_tests.py
search_tests_common.py
seq_tests_common.py PEP8 white space in Tests
test_Ace.py
test_AlignIO.py
test_AlignIO_ClustalIO.py Remove unused import
test_AlignIO_EmbossIO.py Remove unused import
test_AlignIO_FastaIO.py
test_AlignIO_PhylipIO.py Move self-tests to Tests/test_AlignIO_PhylipIO.py + PEP8
test_AlignIO_convert.py
test_Application.py
test_BWA_tool.py
test_BioSQL_MySQLdb.py
test_BioSQL_mysql_connector.py
test_BioSQL_psycopg2.py
test_BioSQL_sqlite3.py
test_CAPS.py
test_CelFile.py Fix PEP8 E3 issues (too few or too many blank lines).
test_Chi2.py
test_ClustalOmega_tool.py
test_Clustalw_tool.py
test_Cluster.py
test_CodonTable.py
test_CodonUsage.py
test_ColorSpiral.py
test_Compass.py
test_Consensus.py PEP8 fixes rest of test files
test_Crystal.py
test_DSSP_tool.py
test_Dialign_tool.py
test_DocSQL.py
test_Emboss.py Misc PEP8 white space cleanup in Tests
test_EmbossPhylipNew.py
test_EmbossPrimer.py
test_Entrez.py
test_Entrez_online.py
test_Enzyme.py
test_FSSP.py
test_Fasttree_tool.py
test_File.py
test_GACrossover.py
test_GAMutation.py
test_GAOrganism.py
test_GAQueens.py
test_GARepair.py
test_GASelection.py
test_GenBank.py
test_GenBank_unittest.py
test_GenomeDiagram.py
test_GraphicsBitmaps.py
test_GraphicsChromosome.py
test_GraphicsDistribution.py
test_GraphicsGeneral.py
test_HMMCasino.py
test_HMMGeneral.py
test_KDTree.py
test_KEGG.py PEP8 on test_KEGG.py
test_KEGG_online.py
test_KGML_graphics.py
test_KGML_graphics_online.py
test_KGML_nographics.py
test_KeyWList.py
test_Location.py
test_LogisticRegression.py
test_MMCIF.py
test_MSAProbs_tool.py
test_Mafft_tool.py
test_MarkovModel.py Fix common PEP8 violation in unittest verbosity argument
test_Medline.py
test_Motif.py
test_Muscle_tool.py
test_NACCESS_tool.py
test_NCBITextParser.py
test_NCBIXML.py
test_NCBI_BLAST_tools.py
test_NCBI_qblast.py
test_NNExclusiveOr.py
test_NNGene.py
test_NNGeneral.py
test_Nexus.py
test_PAML_baseml.py PEP8 fixes, several test files
test_PAML_codeml.py fix more assertions for Python 2.6
test_PAML_tools.py
test_PAML_yn00.py
test_PDB.py assertEquals was deprecated in Python 2.7
test_PDB_KDTree.py
test_ParserSupport.py
test_Pathway.py PEP8 fixes, several test files
test_Phd.py
test_Phylo.py
test_PhyloXML.py PEP8 white space in Tests
test_Phylo_CDAO.py
test_Phylo_NeXML.py
test_Phylo_depend.py
test_PopGen_DFDist.py
test_PopGen_FDist.py
test_PopGen_FDist_nodepend.py
test_PopGen_FastSimCoal.py
test_PopGen_GenePop.py PEP8 fixes, various test files
test_PopGen_GenePop_EasyController.py
test_PopGen_GenePop_nodepend.py Fix common PEP8 violation in unittest verbosity argument
test_PopGen_SimCoal.py
test_PopGen_SimCoal_nodepend.py
test_Prank_tool.py autopep8 E265 - Format block comments.
test_Probcons_tool.py
test_ProtParam.py
test_QCPSuperimposer.py
test_Restriction.py
test_SCOP_Astral.py
test_SCOP_Cla.py PEP8 white space in Tests
test_SCOP_Des.py
test_SCOP_Dom.py
test_SCOP_Hie.py PEP8 white space in Tests
test_SCOP_Raf.py
test_SCOP_Residues.py
test_SCOP_Scop.py
test_SCOP_online.py
test_SVDSuperimposer.py
test_SearchIO_blast_tab.py PEP8 fixes, various test files
test_SearchIO_blast_tab_index.py
test_SearchIO_blast_text.py Test evil dash line in NCBI BLAST text parser
test_SearchIO_blast_xml.py
test_SearchIO_blast_xml_index.py Fix common PEP8 violation in unittest verbosity argument
test_SearchIO_blat_psl.py
test_SearchIO_blat_psl_index.py
test_SearchIO_exonerate.py
test_SearchIO_exonerate_text_index.py Fix common PEP8 violation in unittest verbosity argument
test_SearchIO_exonerate_vulgar_index.py
test_SearchIO_fasta_m10.py
test_SearchIO_fasta_m10_index.py
test_SearchIO_hmmer2_text.py
test_SearchIO_hmmer2_text_index.py Fix common PEP8 violation in unittest verbosity argument
test_SearchIO_hmmer3_domtab.py
test_SearchIO_hmmer3_domtab_index.py
test_SearchIO_hmmer3_tab.py PEP8 fixes, various test files
test_SearchIO_hmmer3_tab_index.py
test_SearchIO_hmmer3_text.py
test_SearchIO_hmmer3_text_index.py
test_SearchIO_model.py
test_SearchIO_write.py
test_SeqIO.py
test_SeqIO_AbiIO.py
test_SeqIO_FastaIO.py
test_SeqIO_Insdc.py
test_SeqIO_PdbIO.py
test_SeqIO_QualityIO.py
test_SeqIO_SeqXML.py
test_SeqIO_convert.py PEP8 white space in Tests
test_SeqIO_features.py
test_SeqIO_index.py
test_SeqIO_online.py
test_SeqIO_write.py
test_SeqRecord.py
test_SeqUtils.py
test_Seq_objs.py
test_SffIO.py
test_SubsMat.py
test_SwissProt.py
test_TCoffee_tool.py PEP8 white space in Tests
test_TogoWS.py
test_TreeConstruction.py
test_Tutorial.py
test_UniGene.py
test_Uniprot.py SwissProt/UniProt example with semi-colon in gene name
test_Wise.py changed a few assertTrue(False) -> fail()
test_XXmotif_tool.py PEP8 fixes, various test files
test_align.py PEP8 fixes, various test files
test_bgzf.py
test_codonalign.py
test_geo.py
test_kNN.py
test_lowess.py
test_motifs.py
test_pairwise2.py
test_phyml_tool.py PEP8 white space in Tests
test_prodoc.py
test_prosite1.py
test_prosite2.py
test_psw.py
test_py3k.py Fix common PEP8 violation in unittest verbosity argument
test_raxml_tool.py
test_samtools_tool.py
test_seq.py
test_translate.py
test_trie.py PEP8 white space in Tests
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