CONTRIB.rst
CONTRIBUTING.rst
DEPRECATED.rst
LICENSE
LICENSE.rst
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NEWS.rst
README.rst
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Bio/SCOP/Cla.py
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Bio/SearchIO/_index.py
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Bio/SearchIO/BlastIO/blast_tab.py
Bio/SearchIO/BlastIO/blast_text.py
Bio/SearchIO/BlastIO/blast_xml.py
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Bio/SeqUtils/CodonUsage.py
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Bio/SeqUtils/IsoelectricPoint.py
Bio/SeqUtils/MeltingTemp.py
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Bio/SeqUtils/lcc.py
Bio/Sequencing/Ace.py
Bio/Sequencing/Phd.py
Bio/Sequencing/__init__.py
Bio/Sequencing/Applications/_Novoalign.py
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Bio/SwissProt/KeyWList.py
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Bio/TogoWS/__init__.py
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Bio/UniProt/GOA.py
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Bio/motifs/clusterbuster.py
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Bio/motifs/meme.py
Bio/motifs/minimal.py
Bio/motifs/pfm.py
Bio/motifs/thresholds.py
Bio/motifs/transfac.py
Bio/motifs/xms.py
Bio/motifs/applications/__init__.py
Bio/motifs/applications/_xxmotif.py
Bio/motifs/jaspar/__init__.py
Bio/motifs/jaspar/db.py
Bio/phenotype/__init__.py
Bio/phenotype/phen_micro.py
Bio/phenotype/pm_fitting.py
BioSQL/BioSeq.py
BioSQL/BioSeqDatabase.py
BioSQL/DBUtils.py
BioSQL/Loader.py
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Doc/Makefile
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Scripts/query_pubmed.py
Scripts/scop_pdb.py
Scripts/update_ncbi_codon_table.py
Scripts/GenBank/check_output.py
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Scripts/PDB/generate_three_to_one_dict.py
Scripts/PDB/hsexpo.py
Scripts/Performance/biosql_performance_load.py
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Scripts/Restriction/ranacompiler.py
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Scripts/SeqGui/SeqGui.py
Scripts/xbbtools/README
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Scripts/xbbtools/xbb_blast.py
Scripts/xbbtools/xbb_blastbg.py
Scripts/xbbtools/xbb_help.py
Scripts/xbbtools/xbb_search.py
Scripts/xbbtools/xbb_translations.py
Scripts/xbbtools/xbb_utils.py
Scripts/xbbtools/xbb_widget.py
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Tests/.coveragerc
Tests/biosql.ini.appveyor
Tests/biosql.ini.sample
Tests/common_BioSQL.py
Tests/common_BioSQL_online.py
Tests/out.bam
Tests/pairwise2_testCases.py
Tests/requires_internet.py
Tests/run_tests.py
Tests/search_tests_common.py
Tests/seq_tests_common.py
Tests/test_Ace.py
Tests/test_Affy.py
Tests/test_AlignIO.py
Tests/test_AlignIO_ClustalIO.py
Tests/test_AlignIO_EmbossIO.py
Tests/test_AlignIO_FastaIO.py
Tests/test_AlignIO_MauveIO.py
Tests/test_AlignIO_PhylipIO.py
Tests/test_AlignIO_convert.py
Tests/test_AlignInfo.py
Tests/test_Align_Alignment.py
Tests/test_Align_a2m.py
Tests/test_Align_bed.py
Tests/test_Align_bigbed.py
Tests/test_Align_bigmaf.py
Tests/test_Align_bigpsl.py
Tests/test_Align_clustal.py
Tests/test_Align_emboss.py
Tests/test_Align_exonerate.py
Tests/test_Align_fasta.py
Tests/test_Align_hhr.py
Tests/test_Align_maf.py
Tests/test_Align_mauve.py
Tests/test_Align_msf.py
Tests/test_Align_nexus.py
Tests/test_Align_phylip.py
Tests/test_Align_psl.py
Tests/test_Align_sam.py
Tests/test_Align_stockholm.py
Tests/test_Align_tabular.py
Tests/test_Application.py
Tests/test_BWA_tool.py
Tests/test_BioSQL_MySQLdb.py
Tests/test_BioSQL_MySQLdb_online.py
Tests/test_BioSQL_mysql_connector.py
Tests/test_BioSQL_mysql_connector_online.py
Tests/test_BioSQL_psycopg2.py
Tests/test_BioSQL_psycopg2_online.py
Tests/test_BioSQL_sqlite3.py
Tests/test_BioSQL_sqlite3_online.py
Tests/test_Blast_Record.py
Tests/test_CAPS.py
Tests/test_Chi2.py
Tests/test_ClustalOmega_tool.py
Tests/test_Clustalw_tool.py
Tests/test_Cluster.py
Tests/test_CodonTable.py
Tests/test_ColorSpiral.py
Tests/test_Compass.py
Tests/test_Consensus.py
Tests/test_Dialign_tool.py
Tests/test_EMBL_unittest.py
Tests/test_Emboss.py
Tests/test_EmbossPhylipNew.py
Tests/test_EmbossPrimer.py
Tests/test_Entrez.py
Tests/test_Entrez_online.py
Tests/test_Entrez_parser.py
Tests/test_Enzyme.py
Tests/test_ExPASy.py
Tests/test_Fasttree_tool.py
Tests/test_File.py
Tests/test_GenBank.py
Tests/test_GenomeDiagram.py
Tests/test_GraphicsBitmaps.py
Tests/test_GraphicsChromosome.py
Tests/test_GraphicsDistribution.py
Tests/test_GraphicsGeneral.py
Tests/test_HMMCasino.py
Tests/test_HMMGeneral.py
Tests/test_KEGG.py
Tests/test_KEGG_online.py
Tests/test_KGML_graphics.py
Tests/test_KGML_graphics_online.py
Tests/test_KGML_nographics.py
Tests/test_KeyWList.py
Tests/test_LogisticRegression.py
Tests/test_MSAProbs_tool.py
Tests/test_MafIO_index.py
Tests/test_Mafft_tool.py
Tests/test_MarkovModel.py
Tests/test_Medline.py
Tests/test_Muscle_tool.py
Tests/test_NCBITextParser.py
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Tests/test_Phylo.py
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Tests/test_Phylo_CDAO.py
Tests/test_Phylo_NeXML.py
Tests/test_Phylo_matplotlib.py
Tests/test_Phylo_networkx.py
Tests/test_PopGen_GenePop.py
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Tests/test_Prank_tool.py
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Tests/test_RCSBFormats.py
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Tests/test_Tutorial.py
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Tests/Abi/A6_1-DB3.ab1
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Tests/Abi/fake.ab1
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Tests/Abi/nonascii_encoding.ab1
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Tests/Blast/text_2226_blastn_003.txt
Tests/Blast/text_2226_blastn_004.txt
Tests/Blast/text_2226_blastp_001.txt
Tests/Blast/text_2226_blastp_002.txt
Tests/Blast/text_2226_blastp_003.txt
Tests/Blast/text_2226_blastp_004.txt
Tests/Blast/text_2226_blastx_001.txt
Tests/Blast/text_2226_blastx_002.txt
Tests/Blast/text_2226_blastx_003.txt
Tests/Blast/text_2226_blastx_004.txt
Tests/Blast/text_2226_tblastn_001.txt
Tests/Blast/text_2226_tblastn_002.txt
Tests/Blast/text_2226_tblastn_003.txt
Tests/Blast/text_2226_tblastn_004.txt
Tests/Blast/text_2226_tblastx_001.txt
Tests/Blast/text_2226_tblastx_002.txt
Tests/Blast/text_2226_tblastx_003.txt
Tests/Blast/text_2226_tblastx_004.txt
Tests/Blast/text_2230_blastp_001.txt
Tests/Blast/wnts.xml
Tests/Blast/wnts.xml.bgz
Tests/Blast/xml_2212L_blastn_001.xml
Tests/Blast/xml_2212L_blastp_001.xml
Tests/Blast/xml_2212L_blastx_001.xml
Tests/Blast/xml_2212L_tblastn_001.xml
Tests/Blast/xml_2212L_tblastx_001.xml
Tests/Blast/xml_2218L_blastp_001.xml
Tests/Blast/xml_2218L_rpsblast_001.xml
Tests/Blast/xml_2218_blastp_001.xml
Tests/Blast/xml_2218_blastp_002.xml
Tests/Blast/xml_2222_blastp_001.xml
Tests/Blast/xml_2222_blastx_001.xml
Tests/Blast/xml_2226_blastn_001.xml
Tests/Blast/xml_2226_blastn_002.xml
Tests/Blast/xml_2226_blastn_003.xml
Tests/Blast/xml_2226_blastn_004.xml
Tests/Blast/xml_2226_blastn_005.xml
Tests/Blast/xml_2226_blastn_006.xml
Tests/Blast/xml_2226_blastp_001.xml
Tests/Blast/xml_2226_blastp_002.xml
Tests/Blast/xml_2226_blastp_003.xml
Tests/Blast/xml_2226_blastp_004.xml
Tests/Blast/xml_2226_blastp_005.xml
Tests/Blast/xml_2226_blastx_001.xml
Tests/Blast/xml_2226_blastx_002.xml
Tests/Blast/xml_2226_blastx_003.xml
Tests/Blast/xml_2226_blastx_004.xml
Tests/Blast/xml_2226_tblastn_001.xml
Tests/Blast/xml_2226_tblastn_002.xml
Tests/Blast/xml_2226_tblastn_003.xml
Tests/Blast/xml_2226_tblastn_004.xml
Tests/Blast/xml_2226_tblastn_005.xml
Tests/Blast/xml_2226_tblastx_001.xml
Tests/Blast/xml_2226_tblastx_002.xml
Tests/Blast/xml_2226_tblastx_003.xml
Tests/Blast/xml_2226_tblastx_004.xml
Tests/Blast/xml_2900_blastn_001.xml
Tests/Blast/xml_2900_blastn_001_v2.xml
Tests/Blast/xml_2900_blastp_001.xml
Tests/Blast/xml_2900_blastp_001_v2.xml
Tests/Blast/xml_2900_blastx_001.xml
Tests/Blast/xml_2900_blastx_001_v2.xml
Tests/Blast/xml_2900_tblastn_001.xml
Tests/Blast/xml_2900_tblastn_001_v2.xml
Tests/Blast/xml_2900_tblastx_001.xml
Tests/Blast/xml_2900_tblastx_001_v2.xml
Tests/Blat/CAG33136.1.fasta
Tests/Blat/README.txt
Tests/Blat/balAcu1.fa
Tests/Blat/bed12.bb
Tests/Blat/bed12.bed
Tests/Blat/bed3.bb
Tests/Blat/bed3.bed
Tests/Blat/bed4.bb
Tests/Blat/bed4.bed
Tests/Blat/bed5.bb
Tests/Blat/bed5.bed
Tests/Blat/bed6.bb
Tests/Blat/bed6.bed
Tests/Blat/bed7.bb
Tests/Blat/bed7.bed
Tests/Blat/bed8.bb
Tests/Blat/bed8.bed
Tests/Blat/bed9.bb
Tests/Blat/bed9.bed
Tests/Blat/bigPsl.bb
Tests/Blat/bigbed_extended.bb
Tests/Blat/bigbedtest.bb
Tests/Blat/bigbedtest.psl.bb
Tests/Blat/dna.fa
Tests/Blat/dna_rna.bb
Tests/Blat/dna_rna.bed
Tests/Blat/dna_rna.psl
Tests/Blat/dna_rna.psl.bb
Tests/Blat/dna_rna.sam
Tests/Blat/fasta_34.fa
Tests/Blat/hg38.fa
Tests/Blat/mirna.pslx
Tests/Blat/psl_34_001.bb
Tests/Blat/psl_34_001.bed
Tests/Blat/psl_34_001.psl
Tests/Blat/psl_34_001.psl.bb
Tests/Blat/psl_34_001.sam
Tests/Blat/psl_34_002.psl
Tests/Blat/psl_34_003.bb
Tests/Blat/psl_34_003.bed
Tests/Blat/psl_34_003.psl
Tests/Blat/psl_34_003.psl.bb
Tests/Blat/psl_34_003.sam
Tests/Blat/psl_34_004.bb
Tests/Blat/psl_34_004.bed
Tests/Blat/psl_34_004.psl
Tests/Blat/psl_34_004.psl.bb
Tests/Blat/psl_34_004.sam
Tests/Blat/psl_34_005.bb
Tests/Blat/psl_34_005.bed
Tests/Blat/psl_34_005.psl
Tests/Blat/psl_34_005.psl.bb
Tests/Blat/psl_34_005.sam
Tests/Blat/psl_35_001.bb
Tests/Blat/psl_35_001.bed
Tests/Blat/psl_35_001.psl
Tests/Blat/psl_35_001.psl.bb
Tests/Blat/psl_35_002.bed
Tests/Blat/psl_35_002.psl
Tests/Blat/psl_35_002.psl.bb
Tests/Blat/pslx_34_001.pslx
Tests/Blat/pslx_34_002.pslx
Tests/Blat/pslx_34_003.pslx
Tests/Blat/pslx_34_004.pslx
Tests/Blat/pslx_34_005.pslx
Tests/Blat/pslx_35_001.pslx
Tests/Blat/pslx_35_002.pslx
Tests/Blat/rna.fa
Tests/CDAO/test.cdao
Tests/Cellosaurus/cell_lines_1.txt
Tests/Cellosaurus/cell_lines_2.txt
Tests/Cellosaurus/cell_lines_3.txt
Tests/Clustalw/clustalw.a2m
Tests/Clustalw/clustalw.aln
Tests/Clustalw/clustalw.fa
Tests/Clustalw/hedgehog.aln
Tests/Clustalw/kalign.a2m
Tests/Clustalw/kalign.aln
Tests/Clustalw/kalign.fa
Tests/Clustalw/msaprobs.a2m
Tests/Clustalw/msaprobs.aln
Tests/Clustalw/msaprobs.fa
Tests/Clustalw/muscle.a2m
Tests/Clustalw/muscle.aln
Tests/Clustalw/muscle.fa
Tests/Clustalw/odd_consensus.aln
Tests/Clustalw/opuntia.aln
Tests/Clustalw/probcons.a2m
Tests/Clustalw/probcons.aln
Tests/Clustalw/probcons.fa
Tests/Clustalw/promals3d.aln
Tests/Clustalw/protein.aln
Tests/Cluster/README
Tests/Cluster/cyano.txt
Tests/CodonUsage/HighlyExpressedGenes.txt
Tests/Compass/comtest1
Tests/Compass/comtest2
Tests/EMBL/101ma_no_coords.embl
Tests/EMBL/A04195.imgt
Tests/EMBL/AAA03323.embl
Tests/EMBL/AE017046.embl
Tests/EMBL/DD231055_edited.embl
Tests/EMBL/DD231055_edited2.embl
Tests/EMBL/DS830848.embl
Tests/EMBL/Human_contigs.embl
Tests/EMBL/RepBase23.02.embl
Tests/EMBL/SC10H5.embl
Tests/EMBL/TRBG361.embl
Tests/EMBL/U87107.embl
Tests/EMBL/embl_with_0_line.embl
Tests/EMBL/epo_prt_selection.embl
Tests/EMBL/hla_3260_sample.imgt
Tests/EMBL/kipo_prt_sample.embl
Tests/EMBL/location_wrap.embl
Tests/EMBL/patents.embl
Tests/EMBL/xx_after_co.embl
Tests/Emboss/NirK.primer3
Tests/Emboss/NirK_full.primer3
Tests/Emboss/alignret.txt
Tests/Emboss/bac_find.primer3
Tests/Emboss/bac_find.psearch
Tests/Emboss/cds_forward.primer3
Tests/Emboss/cds_reverse.primer3
Tests/Emboss/emboss_pair_aln_full_blank_line.txt
Tests/Emboss/internal_oligo.primer3
Tests/Emboss/matcher_pair.txt
Tests/Emboss/matcher_simple.txt
Tests/Emboss/needle.txt
Tests/Emboss/needle_asis.txt
Tests/Emboss/needle_nobrief_multiple.pair
Tests/Emboss/needle_overhang.txt
Tests/Emboss/no_oligo.primer3
Tests/Emboss/short.primer3
Tests/Emboss/water.txt
Tests/Emboss/water2.txt
Tests/Emboss/water_reverse1.txt
Tests/Emboss/water_reverse2.txt
Tests/Emboss/water_reverse3.txt
Tests/Emboss/water_reverse4.txt
Tests/Entrez/biosample.xml
Tests/Entrez/efetch_pmc.xml
Tests/Entrez/efetch_schemas.xml
Tests/Entrez/egquery1.xml
Tests/Entrez/egquery2.xml
Tests/Entrez/einfo1.xml
Tests/Entrez/einfo2.xml
Tests/Entrez/einfo3.xml
Tests/Entrez/einfo4.xml
Tests/Entrez/elink1.xml
Tests/Entrez/elink2.xml
Tests/Entrez/elink3.xml
Tests/Entrez/elink4.xml
Tests/Entrez/elink5.xml
Tests/Entrez/elink6.xml
Tests/Entrez/elink7.xml
Tests/Entrez/elink8.xml
Tests/Entrez/epost1.xml
Tests/Entrez/epost2.xml
Tests/Entrez/epost3.xml
Tests/Entrez/esearch1.xml
Tests/Entrez/esearch2.xml
Tests/Entrez/esearch3.xml
Tests/Entrez/esearch4.xml
Tests/Entrez/esearch5.xml
Tests/Entrez/esearch6.xml
Tests/Entrez/esearch7.xml
Tests/Entrez/esearch8.xml
Tests/Entrez/espell.xml
Tests/Entrez/esummary1.xml
Tests/Entrez/esummary2.xml
Tests/Entrez/esummary3.xml
Tests/Entrez/esummary4.xml
Tests/Entrez/esummary5.xml
Tests/Entrez/esummary6.xml
Tests/Entrez/esummary7.xml
Tests/Entrez/esummary8.xml
Tests/Entrez/esummary9.xml
Tests/Entrez/journals.xml
Tests/Entrez/ncbi_mim.xml
Tests/Entrez/nucleotide1.xml
Tests/Entrez/nucleotide2.xml
Tests/Entrez/protein.xml
Tests/Entrez/pubmed1.xml
Tests/Entrez/pubmed2.xml
Tests/Entrez/pubmed3.html
Tests/Entrez/pubmed4.xml
Tests/Entrez/pubmed5.xml
Tests/Entrez/pubmed6.xml
Tests/Entrez/pubmed7.xml
Tests/Entrez/taxonomy.xml
Tests/Enzymes/lactate.txt
Tests/Enzymes/lipoprotein.txt
Tests/Enzymes/proline.txt
Tests/Enzymes/valine.txt
Tests/Exonerate/README.txt
Tests/Exonerate/exn_22_m_affine_local.exn
Tests/Exonerate/exn_22_m_affine_local_cigar.exn
Tests/Exonerate/exn_22_m_affine_local_vulgar.exn
Tests/Exonerate/exn_22_m_cdna2genome.exn
Tests/Exonerate/exn_22_m_cdna2genome_cigar.exn
Tests/Exonerate/exn_22_m_cdna2genome_vulgar.exn
Tests/Exonerate/exn_22_m_cigar_fshifts.exn
Tests/Exonerate/exn_22_m_coding2coding.exn
Tests/Exonerate/exn_22_m_coding2coding_cigar.exn
Tests/Exonerate/exn_22_m_coding2coding_fshifts.exn
Tests/Exonerate/exn_22_m_coding2coding_vulgar.exn
Tests/Exonerate/exn_22_m_coding2genome.exn
Tests/Exonerate/exn_22_m_coding2genome_cigar.exn
Tests/Exonerate/exn_22_m_coding2genome_vulgar.exn
Tests/Exonerate/exn_22_m_dna2protein.exn
Tests/Exonerate/exn_22_m_dna2protein_cigar.exn
Tests/Exonerate/exn_22_m_dna2protein_vulgar.exn
Tests/Exonerate/exn_22_m_est2genome.exn
Tests/Exonerate/exn_22_m_est2genome_cigar.exn
Tests/Exonerate/exn_22_m_est2genome_vulgar.exn
Tests/Exonerate/exn_22_m_genome2genome.exn
Tests/Exonerate/exn_22_m_ner.exn
Tests/Exonerate/exn_22_m_ner_cigar.exn
Tests/Exonerate/exn_22_m_ner_vulgar.exn
Tests/Exonerate/exn_22_m_protein2dna.exn
Tests/Exonerate/exn_22_m_protein2dna_cigar.exn
Tests/Exonerate/exn_22_m_protein2dna_fshifts.exn
Tests/Exonerate/exn_22_m_protein2dna_vulgar.exn
Tests/Exonerate/exn_22_m_protein2genome.exn
Tests/Exonerate/exn_22_m_protein2genome_cigar.exn
Tests/Exonerate/exn_22_m_protein2genome_vulgar.exn
Tests/Exonerate/exn_22_m_ungapped.exn
Tests/Exonerate/exn_22_m_ungapped_cigar.exn
Tests/Exonerate/exn_22_m_ungapped_trans.exn
Tests/Exonerate/exn_22_m_ungapped_trans_cigar.exn
Tests/Exonerate/exn_22_m_ungapped_trans_vulgar.exn
Tests/Exonerate/exn_22_m_ungapped_vulgar.exn
Tests/Exonerate/exn_22_o_cigar_fshifts2.exn
Tests/Exonerate/exn_22_o_vulgar.exn
Tests/Exonerate/exn_22_o_vulgar_cigar.exn
Tests/Exonerate/exn_22_o_vulgar_fshifts.exn
Tests/Exonerate/exn_22_o_vulgar_fshifts2.exn
Tests/Exonerate/exn_22_q_multiple.exn
Tests/Exonerate/exn_22_q_multiple_cigar.exn
Tests/Exonerate/exn_22_q_multiple_vulgar.exn
Tests/Exonerate/exn_22_q_none.exn
Tests/Exonerate/exn_24_m_protein2genome_met_intron.exn
Tests/Exonerate/exn_24_m_protein2genome_met_intron_cigar.exn
Tests/Exonerate/exn_24_m_protein2genome_met_intron_vulgar.exn
Tests/Exonerate/exn_24_m_protein2genome_revcomp_fshifts.exn
Tests/Exonerate/exn_24_m_protein2genome_revcomp_fshifts_cigar.exn
Tests/Exonerate/exn_24_m_protein2genome_revcomp_fshifts_vulgar.exn
Tests/ExtendedPhylip/primates.phyx
Tests/FSSP/1cnv.fssp
Tests/Fasta/README
Tests/Fasta/aster.pro
Tests/Fasta/aster_no_wrap.pro
Tests/Fasta/centaurea.nu
Tests/Fasta/dups.fasta
Tests/Fasta/elderberry.nu
Tests/Fasta/f001
Tests/Fasta/f002
Tests/Fasta/f003
Tests/Fasta/fa01
Tests/Fasta/flowers.pro.gz
Tests/Fasta/lavender.nu
Tests/Fasta/loveliesbleeding.pro
Tests/Fasta/lupine.nu
Tests/Fasta/nucleotide_lib.fa
Tests/Fasta/nucleotide_m8CB.txt
Tests/Fasta/nucleotide_m8CC.txt
Tests/Fasta/output001.m10
Tests/Fasta/output002.m10
Tests/Fasta/output003.m10
Tests/Fasta/output004.m10
Tests/Fasta/output005.m10
Tests/Fasta/output006.m10
Tests/Fasta/output007.m10
Tests/Fasta/output008.m10
Tests/Fasta/output009.m10
Tests/Fasta/output010.m10
Tests/Fasta/output011.m10
Tests/Fasta/output012.m10
Tests/Fasta/output013.m10
Tests/Fasta/output014.m10
Tests/Fasta/output015.m10
Tests/Fasta/output016.m10
Tests/Fasta/phlox.nu
Tests/Fasta/protein_lib.fa
Tests/Fasta/protein_m8CB.txt
Tests/Fasta/protein_m8CC.txt
Tests/Fasta/rose.pro
Tests/Fasta/rosemary.pro
Tests/Fasta/sweetpea.nu
Tests/Fasta/wisteria.nu
Tests/GFF/NC_001422.gbk
Tests/GFF/NC_001802.fna
Tests/GFF/NC_001802lc.fna
Tests/GFF/NC_001802x.fna
Tests/GFF/multi.fna
Tests/Gck/artificial.gck
Tests/GenBank/1MRR_A.gp
Tests/GenBank/DS830848.gb
Tests/GenBank/EU851978.gbk
Tests/GenBank/EU851978_output.gbk
Tests/GenBank/GU949562.1.gb
Tests/GenBank/HM138502.gbk
Tests/GenBank/HM138502_output.gbk
Tests/GenBank/KF527485.gbk
Tests/GenBank/KF527485_output.gbk
Tests/GenBank/NC_000932.faa
Tests/GenBank/NC_000932.gb
Tests/GenBank/NC_000932.gb.bgz
Tests/GenBank/NC_005816.faa
Tests/GenBank/NC_005816.ffn
Tests/GenBank/NC_005816.fna
Tests/GenBank/NC_005816.gb
Tests/GenBank/NC_005816.tsv
Tests/GenBank/NP_416719.gbwithparts
Tests/GenBank/NT_019265.gb
Tests/GenBank/addgene-plasmid-11664-sequence-180430.gbk
Tests/GenBank/addgene-plasmid-39296-sequence-49545.gbk
Tests/GenBank/arab1.gb
Tests/GenBank/bad_loc_wrap.gb
Tests/GenBank/bad_origin_wrap.gb
Tests/GenBank/bad_origin_wrap_CDS.gb
Tests/GenBank/bad_origin_wrap_fuzzy.gb
Tests/GenBank/bad_origin_wrap_linear.gb
Tests/GenBank/blank_seq.gb
Tests/GenBank/cor6_6.gb
Tests/GenBank/cor6_6.gb.bgz
Tests/GenBank/dbsource_wrap.gb
Tests/GenBank/empty_accession.gbk
Tests/GenBank/empty_feature_qualifier.gb
Tests/GenBank/empty_version.gbk
Tests/GenBank/extra_keywords.gb
Tests/GenBank/gbvrl1_start.seq
Tests/GenBank/invalid_locus_line_spacing.gb
Tests/GenBank/invalid_misc_feature.gb
Tests/GenBank/invalid_product.gb
Tests/GenBank/invalid_structured_comment.gb
Tests/GenBank/iro.gb
Tests/GenBank/negative_location.gb
Tests/GenBank/no_end_marker.gb
Tests/GenBank/no_origin_no_end.gb
Tests/GenBank/noref.gb
Tests/GenBank/one_of.gb
Tests/GenBank/origin_line.gb
Tests/GenBank/pBAD30.gb
Tests/GenBank/pri1.gb
Tests/GenBank/protein_refseq.gb
Tests/GenBank/protein_refseq2.gb
Tests/GenBank/qualifier_escaping_read.gb
Tests/GenBank/qualifier_escaping_write.gb
Tests/GenBank/tls_KDHP01000000.gb
Tests/GenBank/tsa_acropora.gb
Tests/GenBank/wrong_sequence_indent.gb
Tests/Geo/GSE16.txt
Tests/Geo/GSM645.txt
Tests/Geo/GSM691.txt
Tests/Geo/GSM700.txt
Tests/Geo/GSM804.txt
Tests/Geo/soft_ex_affy.txt
Tests/Geo/soft_ex_affy_chp.txt
Tests/Geo/soft_ex_dual.txt
Tests/Geo/soft_ex_family.txt
Tests/Geo/soft_ex_platform.txt
Tests/Geo/soft_ex_series.txt
Tests/Graphics/README
Tests/HHsuite/2uvo_hhblits.hhr
Tests/HHsuite/2uvo_hhblits_emptytable.hhr
Tests/HHsuite/2uvo_hhblits_onlyheader.hhr
Tests/HHsuite/2uvo_hhsearch.hhr
Tests/HHsuite/4p79_hhsearch_server_NOssm.hhr
Tests/HHsuite/4y9h_hhsearch_server_NOssm.hhr
Tests/HHsuite/README.txt
Tests/HHsuite/allx.hhr
Tests/HHsuite/hhpred_9590198.hhr
Tests/HHsuite/hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.hhr
Tests/Hmmer/README.txt
Tests/Hmmer/domtab_30_hmmscan_001.out
Tests/Hmmer/domtab_30_hmmscan_002.out
Tests/Hmmer/domtab_30_hmmscan_003.out
Tests/Hmmer/domtab_30_hmmscan_004.out
Tests/Hmmer/domtab_30_hmmsearch_001.out
Tests/Hmmer/domtab_31b1_hmmscan_001.out
Tests/Hmmer/domtab_31b1_hmmsearch_001.out
Tests/Hmmer/tab_30_hmmscan_001.out
Tests/Hmmer/tab_30_hmmscan_002.out
Tests/Hmmer/tab_30_hmmscan_003.out
Tests/Hmmer/tab_30_hmmscan_004.out
Tests/Hmmer/tab_31b1_hmmscan_001.out
Tests/Hmmer/tab_31b1_hmmsearch_001.out
Tests/Hmmer/text_20_hmmsearch_001.out
Tests/Hmmer/text_21_hmmpfam_001.out
Tests/Hmmer/text_22_hmmpfam_001.out
Tests/Hmmer/text_22_hmmsearch_001.out
Tests/Hmmer/text_23_hmmpfam_001.out
Tests/Hmmer/text_23_hmmpfam_002.out
Tests/Hmmer/text_23_hmmpfam_003.out
Tests/Hmmer/text_23_hmmpfam_004.out
Tests/Hmmer/text_24_hmmpfam_001.out
Tests/Hmmer/text_30_hmmscan_001.out
Tests/Hmmer/text_30_hmmscan_002.out
Tests/Hmmer/text_30_hmmscan_003.out
Tests/Hmmer/text_30_hmmscan_004.out
Tests/Hmmer/text_30_hmmscan_005.out
Tests/Hmmer/text_30_hmmscan_006.out
Tests/Hmmer/text_30_hmmscan_007.out
Tests/Hmmer/text_30_hmmscan_008.out
Tests/Hmmer/text_30_hmmscan_009.out
Tests/Hmmer/text_30_hmmscan_010.out
Tests/Hmmer/text_30_hmmsearch_001.out
Tests/Hmmer/text_30_hmmsearch_002.out
Tests/Hmmer/text_30_hmmsearch_003.out
Tests/Hmmer/text_30_hmmsearch_004.out
Tests/Hmmer/text_30_hmmsearch_005.out
Tests/Hmmer/text_31b1_hmmscan_001.out
Tests/Hmmer/text_31b1_hmmsearch_001.out
Tests/Hmmer/text_31b2_hmmscan_001.out
Tests/Hmmer/text_31b2_hmmsearch_001.out
Tests/Hmmer/text_31b2_hmmsearch_002.out
Tests/Hmmer/text_31b2_phmmer_001.out
Tests/IntelliGenetics/TAT_mase_nuc.txt
Tests/IntelliGenetics/VIF_mase-pro.txt
Tests/IntelliGenetics/vpu_nucaligned.txt
Tests/InterProScan/test_001.xml
Tests/KEGG/compound.irregular
Tests/KEGG/compound.sample
Tests/KEGG/enzyme.4letter
Tests/KEGG/enzyme.irregular
Tests/KEGG/enzyme.new
Tests/KEGG/enzyme.sample
Tests/KEGG/gene.sample
Tests/KEGG/ko00010.xml
Tests/KEGG/ko00253.xml
Tests/KEGG/ko01100.xml
Tests/KEGG/ko03070.xml
Tests/KEGG/map00950.rea
Tests/KEGG/map01100.png
Tests/KEGG/map03070.png
Tests/MAF/bug2453.maf
Tests/MAF/bundle_without_target.bb
Tests/MAF/bundle_without_target.maf
Tests/MAF/cnksr3.fa
Tests/MAF/corrupt.idx
Tests/MAF/humor.maf
Tests/MAF/invalid.idx
Tests/MAF/length_coords_mismatch.maf
Tests/MAF/ucsc_mm9_chr10.bb
Tests/MAF/ucsc_mm9_chr10.maf
Tests/MAF/ucsc_mm9_chr10.mafindex
Tests/MAF/ucsc_mm9_chr10_bad.maf
Tests/MAF/ucsc_mm9_chr10_bad.mafindex
Tests/MAF/ucsc_mm9_chr10_big.maf
Tests/MAF/ucsc_mm9_chr10_big.mafindex
Tests/MAF/ucsc_test.bb
Tests/MAF/ucsc_test.maf
Tests/MAF/unfinished.idx
Tests/MAF/wrong_version.idx
Tests/Mauve/canFam2.fa
Tests/Mauve/combined.fa
Tests/Mauve/combined.xmfa
Tests/Mauve/combined.xmfa.backbone
Tests/Mauve/combined.xmfa.bbcols
Tests/Mauve/equCab1.fa
Tests/Mauve/mm9.fa
Tests/Mauve/separate.xmfa
Tests/Mauve/separate.xmfa.backbone
Tests/Mauve/separate.xmfa.bbcols
Tests/Mauve/simple.fa
Tests/Mauve/simple.xmfa
Tests/Mauve/simple.xmfa.backbone
Tests/Mauve/simple.xmfa.bbcols
Tests/Mauve/simple_short.xmfa
Tests/Medline/pubmed_result1.txt
Tests/Medline/pubmed_result2.txt
Tests/Medline/pubmed_result3.txt
Tests/MetaTool/Meta3.out
Tests/MetaTool/Meta4.out
Tests/MetaTool/Meta6.out
Tests/MetaTool/Meta7.out
Tests/MetaTool/Meta8.out
Tests/MetaTool/meta.out
Tests/MetaTool/meta2.out
Tests/MetaTool/meta9.out
Tests/NBRF/B_nuc.pir
Tests/NBRF/Cw_prot.pir
Tests/NBRF/DMA_nuc.pir
Tests/NBRF/DMB_prot.pir
Tests/NBRF/clustalw.pir
Tests/NMR/noed.xpk
Tests/NMR/out_example.xpk
Tests/NeXML/characters.xml
Tests/NeXML/edgelabels.xml
Tests/NeXML/meta_taxa.xml
Tests/NeXML/meta_types.xml
Tests/NeXML/nexml.xml
Tests/NeXML/phenoscape.xml
Tests/NeXML/sets.xml
Tests/NeXML/taxa.xml
Tests/NeXML/timetree.xml
Tests/NeXML/tolweb.xml
Tests/NeXML/treebase-record.xml
Tests/NeXML/trees-uris.xml
Tests/NeXML/trees.xml
Tests/NeuralNetwork/enolase.fasta
Tests/NeuralNetwork/repeat.fasta
Tests/Nexus/ByteOrderMarkFile.nwk
Tests/Nexus/bats.nex
Tests/Nexus/codonposset.nex
Tests/Nexus/int_node_labels.nwk
Tests/Nexus/test.new
Tests/Nexus/test_Nexus_input.nex
Tests/Nexus/vSysLab_Ganaspidium_multistate.nex
Tests/Nexus/vSysLab_Heptascelio_no-states_10+chars.nex
Tests/Nexus/vSysLab_Oreiscelio_discrete+continuous.nex
Tests/Nib/test_even.fa
Tests/Nib/test_even_bigendian.nib
Tests/Nib/test_even_littleendian.nib
Tests/Nib/test_odd.fa
Tests/Nib/test_odd_bigendian.nib
Tests/Nib/test_odd_littleendian.nib
Tests/PAML/gen_results.py
Tests/PAML/Alignments/aa_alignment.phylip
Tests/PAML/Alignments/alignment.phylip
Tests/PAML/Alignments/dottednames.phylip
Tests/PAML/Alignments/dottednum.fasta
Tests/PAML/Alignments/longnames.fasta
Tests/PAML/Alignments/lysinYangSwanson2002.nuc
Tests/PAML/Control_files/README.txt
Tests/PAML/Control_files/bad1.ctl
Tests/PAML/Control_files/bad2.ctl
Tests/PAML/Control_files/bad3.ctl
Tests/PAML/Control_files/baseml.ctl
Tests/PAML/Control_files/species.tree
Tests/PAML/Control_files/yn00.ctl
Tests/PAML/Control_files/baseml/SE.ctl
Tests/PAML/Control_files/baseml/alpha1rho1.ctl
Tests/PAML/Control_files/baseml/baseml.ctl
Tests/PAML/Control_files/baseml/model0.ctl
Tests/PAML/Control_files/baseml/model1.ctl
Tests/PAML/Control_files/baseml/model2.ctl
Tests/PAML/Control_files/baseml/model3.ctl
Tests/PAML/Control_files/baseml/model4.ctl
Tests/PAML/Control_files/baseml/model5.ctl
Tests/PAML/Control_files/baseml/model6.ctl
Tests/PAML/Control_files/baseml/model7.ctl
Tests/PAML/Control_files/baseml/model8.ctl
Tests/PAML/Control_files/baseml/nhomo1.ctl
Tests/PAML/Control_files/baseml/nhomo3.ctl
Tests/PAML/Control_files/baseml/nhomo4.ctl
Tests/PAML/Control_files/baseml/nparK1.ctl
Tests/PAML/Control_files/baseml/nparK2.ctl
Tests/PAML/Control_files/baseml/nparK3.ctl
Tests/PAML/Control_files/baseml/nparK4.ctl
Tests/PAML/Control_files/codeml/NSsite3.ctl
Tests/PAML/Control_files/codeml/SE.ctl
Tests/PAML/Control_files/codeml/aa_model0.ctl
Tests/PAML/Control_files/codeml/aa_pairwise.ctl
Tests/PAML/Control_files/codeml/all_NSsites.ctl
Tests/PAML/Control_files/codeml/branchsiteA.ctl
Tests/PAML/Control_files/codeml/clademodelC.ctl
Tests/PAML/Control_files/codeml/codeml.ctl
Tests/PAML/Control_files/codeml/freeratio.ctl
Tests/PAML/Control_files/codeml/m2a_rel.ctl
Tests/PAML/Control_files/codeml/ngene2_mgene02.ctl
Tests/PAML/Control_files/codeml/ngene2_mgene1.ctl
Tests/PAML/Control_files/codeml/ngene2_mgene34.ctl
Tests/PAML/Control_files/codeml/pairwise.ctl
Tests/PAML/Control_files/yn00/yn00.ctl
Tests/PAML/Control_files/yn00/yn00_dotted.ctl
Tests/PAML/Control_files/yn00/yn00_dottednum.ctl
Tests/PAML/Control_files/yn00/yn00_long.ctl
Tests/PAML/Results/bad_results.out
Tests/PAML/Results/baseml/baseml_SE.out
Tests/PAML/Results/baseml/baseml_alpha1rho1.out
Tests/PAML/Results/baseml/SE/SE-4_1.out
Tests/PAML/Results/baseml/SE/SE-4_3.out
Tests/PAML/Results/baseml/SE/SE-4_4.out
Tests/PAML/Results/baseml/SE/SE-4_4c.out
Tests/PAML/Results/baseml/SE/SE-4_5.out
Tests/PAML/Results/baseml/SE/SE-4_6.out
Tests/PAML/Results/baseml/SE/SE-4_7.out
Tests/PAML/Results/baseml/alpha1rho1/alpha1rho1-4_1.out
Tests/PAML/Results/baseml/alpha1rho1/alpha1rho1-4_6.out
Tests/PAML/Results/baseml/alpha1rho1/alpha1rho1-4_7.out
Tests/PAML/Results/baseml/model/model0-4_1.out
Tests/PAML/Results/baseml/model/model0-4_3.out
Tests/PAML/Results/baseml/model/model0-4_4.out
Tests/PAML/Results/baseml/model/model0-4_4c.out
Tests/PAML/Results/baseml/model/model0-4_5.out
Tests/PAML/Results/baseml/model/model0-4_6.out
Tests/PAML/Results/baseml/model/model0-4_7.out
Tests/PAML/Results/baseml/model/model1-4_1.out
Tests/PAML/Results/baseml/model/model1-4_3.out
Tests/PAML/Results/baseml/model/model1-4_4.out
Tests/PAML/Results/baseml/model/model1-4_4c.out
Tests/PAML/Results/baseml/model/model1-4_5.out
Tests/PAML/Results/baseml/model/model1-4_6.out
Tests/PAML/Results/baseml/model/model1-4_7.out
Tests/PAML/Results/baseml/model/model2-4_1.out
Tests/PAML/Results/baseml/model/model2-4_3.out
Tests/PAML/Results/baseml/model/model2-4_4.out
Tests/PAML/Results/baseml/model/model2-4_4c.out
Tests/PAML/Results/baseml/model/model2-4_5.out
Tests/PAML/Results/baseml/model/model2-4_6.out
Tests/PAML/Results/baseml/model/model2-4_7.out
Tests/PAML/Results/baseml/model/model3-4_1.out
Tests/PAML/Results/baseml/model/model3-4_3.out
Tests/PAML/Results/baseml/model/model3-4_4.out
Tests/PAML/Results/baseml/model/model3-4_4c.out
Tests/PAML/Results/baseml/model/model3-4_5.out
Tests/PAML/Results/baseml/model/model3-4_6.out
Tests/PAML/Results/baseml/model/model3-4_7.out
Tests/PAML/Results/baseml/model/model4-4_1.out
Tests/PAML/Results/baseml/model/model4-4_3.out
Tests/PAML/Results/baseml/model/model4-4_4.out
Tests/PAML/Results/baseml/model/model4-4_4c.out
Tests/PAML/Results/baseml/model/model4-4_5.out
Tests/PAML/Results/baseml/model/model4-4_6.out
Tests/PAML/Results/baseml/model/model4-4_7.out
Tests/PAML/Results/baseml/model/model5-4_1.out
Tests/PAML/Results/baseml/model/model5-4_3.out
Tests/PAML/Results/baseml/model/model5-4_4.out
Tests/PAML/Results/baseml/model/model5-4_4c.out
Tests/PAML/Results/baseml/model/model5-4_5.out
Tests/PAML/Results/baseml/model/model5-4_6.out
Tests/PAML/Results/baseml/model/model5-4_7.out
Tests/PAML/Results/baseml/model/model6-4_1.out
Tests/PAML/Results/baseml/model/model6-4_3.out
Tests/PAML/Results/baseml/model/model6-4_4.out
Tests/PAML/Results/baseml/model/model6-4_4c.out
Tests/PAML/Results/baseml/model/model6-4_5.out
Tests/PAML/Results/baseml/model/model6-4_6.out
Tests/PAML/Results/baseml/model/model6-4_7.out
Tests/PAML/Results/baseml/model/model7-4_1.out
Tests/PAML/Results/baseml/model/model7-4_3.out
Tests/PAML/Results/baseml/model/model7-4_4.out
Tests/PAML/Results/baseml/model/model7-4_4c.out
Tests/PAML/Results/baseml/model/model7-4_5.out
Tests/PAML/Results/baseml/model/model7-4_6.out
Tests/PAML/Results/baseml/model/model7-4_7.out
Tests/PAML/Results/baseml/model/model8-4_1.out
Tests/PAML/Results/baseml/model/model8-4_3.out
Tests/PAML/Results/baseml/model/model8-4_4.out
Tests/PAML/Results/baseml/model/model8-4_4c.out
Tests/PAML/Results/baseml/model/model8-4_5.out
Tests/PAML/Results/baseml/model/model8-4_6.out
Tests/PAML/Results/baseml/model/model8-4_7.out
Tests/PAML/Results/baseml/nhomo/nhomo1-4_1.out
Tests/PAML/Results/baseml/nhomo/nhomo1-4_3.out
Tests/PAML/Results/baseml/nhomo/nhomo1-4_4.out
Tests/PAML/Results/baseml/nhomo/nhomo1-4_4c.out
Tests/PAML/Results/baseml/nhomo/nhomo1-4_5.out
Tests/PAML/Results/baseml/nhomo/nhomo1-4_6.out
Tests/PAML/Results/baseml/nhomo/nhomo1-4_7.out
Tests/PAML/Results/baseml/nhomo/nhomo3-4_1.out
Tests/PAML/Results/baseml/nhomo/nhomo3-4_3.out
Tests/PAML/Results/baseml/nhomo/nhomo3-4_4.out
Tests/PAML/Results/baseml/nhomo/nhomo3-4_4c.out
Tests/PAML/Results/baseml/nhomo/nhomo3-4_5.out
Tests/PAML/Results/baseml/nhomo/nhomo3-4_6.out
Tests/PAML/Results/baseml/nhomo/nhomo3-4_7.out
Tests/PAML/Results/baseml/nhomo/nhomo4-4_1.out
Tests/PAML/Results/baseml/nhomo/nhomo4-4_3.out
Tests/PAML/Results/baseml/nhomo/nhomo4-4_4.out
Tests/PAML/Results/baseml/nhomo/nhomo4-4_4c.out
Tests/PAML/Results/baseml/nhomo/nhomo4-4_5.out
Tests/PAML/Results/baseml/nhomo/nhomo4-4_6.out
Tests/PAML/Results/baseml/nhomo/nhomo4-4_7.out
Tests/PAML/Results/baseml/nparK/nparK1-4_1.out
Tests/PAML/Results/baseml/nparK/nparK1-4_6.out
Tests/PAML/Results/baseml/nparK/nparK1-4_7.out
Tests/PAML/Results/baseml/nparK/nparK2-4_1.out
Tests/PAML/Results/baseml/nparK/nparK2-4_6.out
Tests/PAML/Results/baseml/nparK/nparK2-4_7.out
Tests/PAML/Results/baseml/nparK/nparK3-4_1.out
Tests/PAML/Results/baseml/nparK/nparK3-4_6.out
Tests/PAML/Results/baseml/nparK/nparK3-4_7.out
Tests/PAML/Results/baseml/nparK/nparK4-4_1.out
Tests/PAML/Results/baseml/nparK/nparK4-4_6.out
Tests/PAML/Results/baseml/nparK/nparK4-4_7.out
Tests/PAML/Results/baseml/versions/baseml41.out
Tests/PAML/Results/baseml/versions/baseml43.out
Tests/PAML/Results/baseml/versions/baseml44.out
Tests/PAML/Results/baseml/versions/baseml44c.out
Tests/PAML/Results/codeml/tree_regexp_versatility.out
Tests/PAML/Results/codeml/NSsite3/NSsite3-4_1.out
Tests/PAML/Results/codeml/NSsite3/NSsite3-4_3.out
Tests/PAML/Results/codeml/NSsite3/NSsite3-4_4.out
Tests/PAML/Results/codeml/NSsite3/NSsite3-4_4c.out
Tests/PAML/Results/codeml/NSsite3/NSsite3-4_5.out
Tests/PAML/Results/codeml/SE/SE-4_1.out
Tests/PAML/Results/codeml/SE/SE-4_3.out
Tests/PAML/Results/codeml/SE/SE-4_4.out
Tests/PAML/Results/codeml/SE/SE-4_4c.out
Tests/PAML/Results/codeml/SE/SE-4_5.out
Tests/PAML/Results/codeml/SE/SE-4_6.out
Tests/PAML/Results/codeml/SE/SE-4_7.out
Tests/PAML/Results/codeml/aa_model0/aa_model0-4_1.out
Tests/PAML/Results/codeml/aa_model0/aa_model0-4_3.out
Tests/PAML/Results/codeml/aa_model0/aa_model0-4_4.out
Tests/PAML/Results/codeml/aa_model0/aa_model0-4_4c.out
Tests/PAML/Results/codeml/aa_model0/aa_model0-4_5.out
Tests/PAML/Results/codeml/aa_model0/aa_model0-4_6.out
Tests/PAML/Results/codeml/aa_model0/aa_model0-4_7.out
Tests/PAML/Results/codeml/aa_pairwise/aa_pairwise-4_1.out
Tests/PAML/Results/codeml/aa_pairwise/aa_pairwise-4_3.out
Tests/PAML/Results/codeml/aa_pairwise/aa_pairwise-4_4.out
Tests/PAML/Results/codeml/aa_pairwise/aa_pairwise-4_4c.out
Tests/PAML/Results/codeml/aa_pairwise/aa_pairwise-4_5.out
Tests/PAML/Results/codeml/aa_pairwise/aa_pairwise-4_6.out
Tests/PAML/Results/codeml/aa_pairwise/aa_pairwise-4_7.out
Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_1.out
Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_3.out
Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_4.out
Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_4c.out
Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_5.out
Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_6.out
Tests/PAML/Results/codeml/all_NSsites/all_NSsites-4_7.out
Tests/PAML/Results/codeml/branchsiteA/branchsiteA-4_1.out
Tests/PAML/Results/codeml/branchsiteA/branchsiteA-4_3.out
Tests/PAML/Results/codeml/branchsiteA/branchsiteA-4_4.out
Tests/PAML/Results/codeml/branchsiteA/branchsiteA-4_4c.out
Tests/PAML/Results/codeml/branchsiteA/branchsiteA-4_5.out
Tests/PAML/Results/codeml/branchsiteA/branchsiteA-4_6.out
Tests/PAML/Results/codeml/branchsiteA/branchsiteA-4_7.out
Tests/PAML/Results/codeml/clademodelC/clademodelC-4_1.out
Tests/PAML/Results/codeml/clademodelC/clademodelC-4_3.out
Tests/PAML/Results/codeml/clademodelC/clademodelC-4_4.out
Tests/PAML/Results/codeml/clademodelC/clademodelC-4_4c.out
Tests/PAML/Results/codeml/clademodelC/clademodelC-4_5.out
Tests/PAML/Results/codeml/clademodelC/clademodelC-4_6.out
Tests/PAML/Results/codeml/clademodelC/clademodelC-4_7.out
Tests/PAML/Results/codeml/freeratio/freeratio-4_1.out
Tests/PAML/Results/codeml/freeratio/freeratio-4_3.out
Tests/PAML/Results/codeml/freeratio/freeratio-4_4.out
Tests/PAML/Results/codeml/freeratio/freeratio-4_4c.out
Tests/PAML/Results/codeml/freeratio/freeratio-4_5.out
Tests/PAML/Results/codeml/freeratio/freeratio-4_6.out
Tests/PAML/Results/codeml/freeratio/freeratio-4_7.out
Tests/PAML/Results/codeml/m2a_rel/m2a_rel-4_6.out
Tests/PAML/Results/codeml/m2a_rel/m2a_rel-4_7.out
Tests/PAML/Results/codeml/m2a_rel/m2a_rel-4_8.out
Tests/PAML/Results/codeml/m2a_rel/m2a_rel-4_9a.out
Tests/PAML/Results/codeml/ngene2_mgene02/ngene2_mgene02-4_1.out
Tests/PAML/Results/codeml/ngene2_mgene02/ngene2_mgene02-4_3.out
Tests/PAML/Results/codeml/ngene2_mgene02/ngene2_mgene02-4_4.out
Tests/PAML/Results/codeml/ngene2_mgene02/ngene2_mgene02-4_4c.out
Tests/PAML/Results/codeml/ngene2_mgene02/ngene2_mgene02-4_5.out
Tests/PAML/Results/codeml/ngene2_mgene02/ngene2_mgene02-4_6.out
Tests/PAML/Results/codeml/ngene2_mgene02/ngene2_mgene02-4_7.out
Tests/PAML/Results/codeml/ngene2_mgene1/ngene2_mgene1-4_3.out
Tests/PAML/Results/codeml/ngene2_mgene1/ngene2_mgene1-4_4.out
Tests/PAML/Results/codeml/ngene2_mgene1/ngene2_mgene1-4_4c.out
Tests/PAML/Results/codeml/ngene2_mgene1/ngene2_mgene1-4_5.out
Tests/PAML/Results/codeml/ngene2_mgene34/ngene2_mgene34-4_1.out
Tests/PAML/Results/codeml/ngene2_mgene34/ngene2_mgene34-4_3.out
Tests/PAML/Results/codeml/ngene2_mgene34/ngene2_mgene34-4_4.out
Tests/PAML/Results/codeml/ngene2_mgene34/ngene2_mgene34-4_4c.out
Tests/PAML/Results/codeml/ngene2_mgene34/ngene2_mgene34-4_5.out
Tests/PAML/Results/codeml/ngene2_mgene34/ngene2_mgene34-4_6.out
Tests/PAML/Results/codeml/ngene2_mgene34/ngene2_mgene34-4_7.out
Tests/PAML/Results/codeml/pairwise/pairwise-4_1.out
Tests/PAML/Results/codeml/pairwise/pairwise-4_3.out
Tests/PAML/Results/codeml/pairwise/pairwise-4_4.out
Tests/PAML/Results/codeml/pairwise/pairwise-4_4c.out
Tests/PAML/Results/codeml/pairwise/pairwise-4_5.out
Tests/PAML/Results/codeml/pairwise/pairwise-4_6.out
Tests/PAML/Results/codeml/pairwise/pairwise-4_7.out
Tests/PAML/Results/yn00/yn00-4_1.out
Tests/PAML/Results/yn00/yn00-4_3.out
Tests/PAML/Results/yn00/yn00-4_4.out
Tests/PAML/Results/yn00/yn00-4_4c.out
Tests/PAML/Results/yn00/yn00-4_5.out
Tests/PAML/Results/yn00/yn00-4_6.out
Tests/PAML/Results/yn00/yn00-4_7.out
Tests/PAML/Results/yn00/yn00-4_8.out
Tests/PAML/Results/yn00/yn00_dotted-4_9i.out
Tests/PAML/Results/yn00/yn00_dottednum-4_9i.out
Tests/PAML/Results/yn00/yn00_long-4_8.out
Tests/PAML/Trees/bad.tree
Tests/PAML/Trees/lysin.trees
Tests/PAML/Trees/lysin.trees.4.6
Tests/PAML/Trees/species.tree
Tests/PDB/1A7G.cif
Tests/PDB/1A8O.asa
Tests/PDB/1A8O.cif
Tests/PDB/1A8O.mmtf
Tests/PDB/1A8O.pdb
Tests/PDB/1A8O.rsa
Tests/PDB/1A8O.xyzr
Tests/PDB/1AS5.cif
Tests/PDB/1LCD.cif
Tests/PDB/1LCD.pdb
Tests/PDB/1MOM_min.cif
Tests/PDB/1SSU_mod.cif
Tests/PDB/1SSU_mod.pdb
Tests/PDB/2BEG.cif
Tests/PDB/2BEG.dssp
Tests/PDB/2BEG.pdb
Tests/PDB/2BEG_noheader.dssp
Tests/PDB/2OFG.cif
Tests/PDB/2XHE.cif
Tests/PDB/2XHE.pdb
Tests/PDB/2n0n_M1.pdb
Tests/PDB/3JQH.cif
Tests/PDB/4CUP.cif
Tests/PDB/4CUP.mmtf
Tests/PDB/4Q9R_min.cif
Tests/PDB/4ZHL.cif
Tests/PDB/4ZHL.mmtf
Tests/PDB/6WQA.cif
Tests/PDB/7CFN.cif
Tests/PDB/7CFN_aligned.cif
Tests/PDB/7DDO.pdb
Tests/PDB/Ahmad_RASA.txt
Tests/PDB/Miller_RASA.txt
Tests/PDB/Sander_RASA.txt
Tests/PDB/Wilke_RASA.txt
Tests/PDB/a_structure.cif
Tests/PDB/a_structure.pdb
Tests/PDB/alignment_file.fa
Tests/PDB/d256ba_.ent
Tests/PDB/disordered.pdb
Tests/PDB/dssp_xtra_Sander.txt
Tests/PDB/header.pdb
Tests/PDB/ions.pdb
Tests/PDB/lib_10_z_5.txt
Tests/PDB/occupancy.pdb
Tests/PQR/1A80.pqr
Tests/Phd/phd1
Tests/Phd/phd2
Tests/Phd/phd_454
Tests/Phd/phd_solexa
Tests/Phylip/five.dat
Tests/Phylip/four.dat
Tests/Phylip/hennigian.phy
Tests/Phylip/horses.phy
Tests/Phylip/horses.tree
Tests/Phylip/interlaced.phy
Tests/Phylip/interlaced2.phy
Tests/Phylip/one.dat
Tests/Phylip/random.phy
Tests/Phylip/reference_dna.phy
Tests/Phylip/reference_dna2.phy
Tests/Phylip/sequential.phy
Tests/Phylip/sequential2.phy
Tests/Phylip/six.dat
Tests/Phylip/three.dat
Tests/Phylip/two.dat
Tests/PhyloXML/apaf.xml
Tests/PhyloXML/bcl_2.xml
Tests/PhyloXML/distribution.xml
Tests/PhyloXML/example.xml
Tests/PhyloXML/made_up.xml
Tests/PhyloXML/o_tol_332_d_dollo.xml
Tests/PhyloXML/phyloxml_examples.xml
Tests/PopGen/README
Tests/PopGen/big.gen
Tests/PopGen/c2line.gen
Tests/PopGen/c2space.gen
Tests/PopGen/c3line.gen
Tests/PopGen/c3space.gen
Tests/PopGen/haplo.gen
Tests/PopGen/haplo2.gen
Tests/PopGen/haplo3.gen
Tests/Prosite/ps00107.txt
Tests/Prosite/ps00159.txt
Tests/Prosite/ps00165.txt
Tests/Prosite/ps00432.txt
Tests/Prosite/ps00488.txt
Tests/Prosite/ps00546.txt
Tests/Prosite/Doc/pdoc00100.txt
Tests/Prosite/Doc/pdoc00113.txt
Tests/Prosite/Doc/pdoc00144.txt
Tests/Prosite/Doc/pdoc00149.txt
Tests/Prosite/Doc/pdoc00340.txt
Tests/Prosite/Doc/pdoc00424.txt
Tests/Prosite/Doc/pdoc00472.txt
Tests/Prosite/Doc/pdoc00640.txt
Tests/Prosite/Doc/pdoc00787.txt
Tests/Prosite/Doc/pdoc00933.txt
Tests/Prosite/Doc/prosite.excerpt.doc
Tests/Quality/error_diff_ids.fastq
Tests/Quality/error_double_qual.fastq
Tests/Quality/error_double_seq.fastq
Tests/Quality/error_long_qual.fastq
Tests/Quality/error_no_qual.fastq
Tests/Quality/error_qual_del.fastq
Tests/Quality/error_qual_escape.fastq
Tests/Quality/error_qual_null.fastq
Tests/Quality/error_qual_space.fastq
Tests/Quality/error_qual_tab.fastq
Tests/Quality/error_qual_unit_sep.fastq
Tests/Quality/error_qual_vtab.fastq
Tests/Quality/error_short_qual.fastq
Tests/Quality/error_spaces.fastq
Tests/Quality/error_tabs.fastq
Tests/Quality/error_trunc_at_plus.fastq
Tests/Quality/error_trunc_at_qual.fastq
Tests/Quality/error_trunc_at_seq.fastq
Tests/Quality/error_trunc_in_plus.fastq
Tests/Quality/error_trunc_in_qual.fastq
Tests/Quality/error_trunc_in_seq.fastq
Tests/Quality/error_trunc_in_title.fastq
Tests/Quality/example.fasta
Tests/Quality/example.fastq
Tests/Quality/example.fastq.bgz
Tests/Quality/example.fastq.gz
Tests/Quality/example.qual
Tests/Quality/example_dos.fastq
Tests/Quality/example_dos.fastq.bgz
Tests/Quality/illumina_faked.fastq
Tests/Quality/illumina_full_range_as_illumina.fastq
Tests/Quality/illumina_full_range_as_sanger.fastq
Tests/Quality/illumina_full_range_as_solexa.fastq
Tests/Quality/illumina_full_range_original_illumina.fastq
Tests/Quality/longreads_as_illumina.fastq
Tests/Quality/longreads_as_sanger.fastq
Tests/Quality/longreads_as_solexa.fastq
Tests/Quality/longreads_original_sanger.fastq
Tests/Quality/misc_dna_as_illumina.fastq
Tests/Quality/misc_dna_as_sanger.fastq
Tests/Quality/misc_dna_as_solexa.fastq
Tests/Quality/misc_dna_original_sanger.fastq
Tests/Quality/misc_rna_as_illumina.fastq
Tests/Quality/misc_rna_as_sanger.fastq
Tests/Quality/misc_rna_as_solexa.fastq
Tests/Quality/misc_rna_original_sanger.fastq
Tests/Quality/sanger_93.fastq
Tests/Quality/sanger_faked.fastq
Tests/Quality/sanger_full_range_as_illumina.fastq
Tests/Quality/sanger_full_range_as_sanger.fastq
Tests/Quality/sanger_full_range_as_solexa.fastq
Tests/Quality/sanger_full_range_original_sanger.fastq
Tests/Quality/solexa_example.fastq
Tests/Quality/solexa_faked.fastq
Tests/Quality/solexa_full_range_as_illumina.fastq
Tests/Quality/solexa_full_range_as_sanger.fastq
Tests/Quality/solexa_full_range_as_solexa.fastq
Tests/Quality/solexa_full_range_original_solexa.fastq
Tests/Quality/tricky.fastq
Tests/Quality/wrapping_as_illumina.fastq
Tests/Quality/wrapping_as_sanger.fastq
Tests/Quality/wrapping_as_solexa.fastq
Tests/Quality/wrapping_original_sanger.fastq
Tests/Quality/zero_length.fastq
Tests/Rebase/bamii.htm
Tests/Rebase/bamii.txt
Tests/Rebase/cac81.htm
Tests/Rebase/cac81.txt
Tests/Rebase/crei.htm
Tests/Rebase/crei.txt
Tests/Rebase/foki.htm
Tests/Rebase/foki.txt
Tests/Rebase/pvuii.htm
Tests/Rebase/pvuii.txt
Tests/Rebase/taqi.htm
Tests/Rebase/taqi.txt
Tests/Registry/EDD_RAT.dat
Tests/Registry/bt001
Tests/Registry/seqs.fasta
Tests/Roche/E3MFGYR02_alt_index_at_end.sff
Tests/Roche/E3MFGYR02_alt_index_at_start.sff
Tests/Roche/E3MFGYR02_alt_index_in_middle.sff
Tests/Roche/E3MFGYR02_index_at_start.sff
Tests/Roche/E3MFGYR02_index_in_middle.sff
Tests/Roche/E3MFGYR02_no_manifest.sff
Tests/Roche/E3MFGYR02_random_10_reads.fasta
Tests/Roche/E3MFGYR02_random_10_reads.qual
Tests/Roche/E3MFGYR02_random_10_reads.sff
Tests/Roche/E3MFGYR02_random_10_reads.sff.gz
Tests/Roche/E3MFGYR02_random_10_reads_no_trim.fasta
Tests/Roche/E3MFGYR02_random_10_reads_no_trim.qual
Tests/Roche/README.txt
Tests/Roche/greek.sff
Tests/Roche/invalid_greek_E3MFGYR02.sff
Tests/Roche/invalid_paired_E3MFGYR02.sff
Tests/Roche/paired.sff
Tests/Roche/triple_sff.idx
Tests/Roche/triple_sff_rel_paths.idx
Tests/SCOP/dir.cla.scop.txt_test
Tests/SCOP/dir.des.scop.txt_test
Tests/SCOP/dir.hie.scop.txt_test
Tests/SCOP/raftest.txt
Tests/SCOP/testDom.txt
Tests/SCOP/scopseq-test/astral-scopdom-seqres-all-test.fa
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-10-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-100-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-20-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-25-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-30-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-35-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-40-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-50-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-70-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-90-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-95-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e+0,7-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e+0-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e+1-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-0,3-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-1,3-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-1-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-10-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-15-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-2,3-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-2-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-20-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-25-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-3-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-4-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-5-test.id
Tests/SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-e100m-e-50-test.id
Tests/Saf/saf1.txt
Tests/SamBam/bam1.bam
Tests/SamBam/bam1_sorted.bam
Tests/SamBam/bam2.bam
Tests/SamBam/bam2_sorted.bam
Tests/SamBam/ex1.bam
Tests/SamBam/ex1.fa
Tests/SamBam/ex1.sam
Tests/SamBam/ex1_header.bam
Tests/SamBam/ex1_header.sam
Tests/SamBam/ex1_refresh.bam
Tests/SamBam/readme.txt
Tests/SamBam/sam1.sam
Tests/SamBam/sam2.sam
Tests/SeqXML/corrupt_example1.xml
Tests/SeqXML/corrupt_example2.xml
Tests/SeqXML/dna_example.xml
Tests/SeqXML/global_species_example.xml
Tests/SeqXML/protein_example.xml
Tests/SeqXML/rna_example.xml
Tests/SnapGene/pFA-KanMX4.dna
Tests/SnapGene/sample-d.dna
Tests/SnapGene/sample-e.dna
Tests/SnapGene/sample-f.dna
Tests/Stockholm/cath1.sth
Tests/Stockholm/cath2.sth
Tests/Stockholm/cath3.sth
Tests/Stockholm/example.sth
Tests/Stockholm/funny.sth
Tests/Stockholm/globins45.ali
Tests/Stockholm/pfam1.seed.txt
Tests/Stockholm/pfam2.seed.txt
Tests/Stockholm/pfam3.seed.txt
Tests/Stockholm/pfam4.seed.txt
Tests/Stockholm/pfam5.seed.txt
Tests/Stockholm/pfam6.seed.txt
Tests/Stockholm/pfam7.seed.txt
Tests/Stockholm/pfam8.seed.txt
Tests/Stockholm/pfam9.seed.txt
Tests/Stockholm/rfam1.seed.txt
Tests/Stockholm/rfam2.seed.txt
Tests/Stockholm/rfam3.seed.txt
Tests/Stockholm/rfam4.seed.txt
Tests/Stockholm/rfam5.seed.txt
Tests/Stockholm/simple.sth
Tests/SubsMat/aaDistrib.txt
Tests/SubsMat/acc_rep_mat.pik
Tests/SubsMat/protein_count.txt
Tests/SubsMat/protein_freq.txt
Tests/SubsMat/redAADistrib.txt
Tests/SubsMat/redAltAADistrib.txt
Tests/SwissProt/F2CXE6.txt
Tests/SwissProt/F2CXE6.xml
Tests/SwissProt/H2CNN8.txt
Tests/SwissProt/H2CNN8.xml
Tests/SwissProt/O23729.txt
Tests/SwissProt/O95832.txt
Tests/SwissProt/P04439.txt
Tests/SwissProt/P0A186.txt
Tests/SwissProt/P0CK95.txt
Tests/SwissProt/P16235.txt
Tests/SwissProt/P39896.txt
Tests/SwissProt/P60137.txt
Tests/SwissProt/P60904.txt
Tests/SwissProt/P62258.txt
Tests/SwissProt/P68308.txt
Tests/SwissProt/P84001.xml
Tests/SwissProt/P97881.xml
Tests/SwissProt/Q13454.txt
Tests/SwissProt/Q13639.txt
Tests/SwissProt/Q13639.xml
Tests/SwissProt/Q7Z739.txt
Tests/SwissProt/R5HY77.xml
Tests/SwissProt/README
Tests/SwissProt/keywlist.txt
Tests/SwissProt/keywlist2.txt
Tests/SwissProt/multi_ex.fasta
Tests/SwissProt/multi_ex.gff
Tests/SwissProt/multi_ex.list
Tests/SwissProt/multi_ex.rdf
Tests/SwissProt/multi_ex.txt
Tests/SwissProt/multi_ex.xml
Tests/SwissProt/sp012
Tests/SwissProt/sp013
Tests/SwissProt/sp015
Tests/SwissProt/sp016
Tests/SwissProt/uni001
Tests/SwissProt/uni002
Tests/SwissProt/uni003
Tests/TreeConstruction/adam_refs.tre
Tests/TreeConstruction/consensus_refs.tre
Tests/TreeConstruction/majority_ref.tre
Tests/TreeConstruction/msa.phy
Tests/TreeConstruction/neighbor_trees.tre
Tests/TreeConstruction/nj.tre
Tests/TreeConstruction/nj_min.tre
Tests/TreeConstruction/pars3.tre
Tests/TreeConstruction/strict_refs.tre
Tests/TreeConstruction/test.log
Tests/TreeConstruction/trees.tre
Tests/TreeConstruction/upgma.tre
Tests/TwoBit/sequence.bigendian.2bit
Tests/TwoBit/sequence.fa
Tests/TwoBit/sequence.littleendian.2bit
Tests/TwoBit/sequence.long.2bit
Tests/UniGene/Eca.1.2425.data
Tests/UniGene/Hs.2.data
Tests/UniGene/Mdm_partial.data
Tests/UniProt/gene_association.goa_yeast.1.gaf
Tests/UniProt/goa_human_sample.gpi
Tests/UniProt/goa_yeast.gaf
Tests/UniProt/goa_yeast.gpa.59.gpa
Tests/UniProt/gp_information.goa_yeast.28.gpi
Tests/Wise/human_114_g01_exons.fna_01
Tests/Wise/human_114_g02_exons.fna_01
Tests/Xdna/sample-a.xdna
Tests/Xdna/sample-b.xdna
Tests/Xdna/sample-c.xprt
Tests/codonalign/adh.aln
Tests/codonalign/drosophilla.fasta
Tests/codonalign/egfr_id
Tests/codonalign/egfr_nucl.fa
Tests/codonalign/egfr_pro.aln
Tests/codonalign/nucl1.fa
Tests/codonalign/nucl2.fa
Tests/codonalign/nucl3.fa
Tests/codonalign/nucl4.fa
Tests/codonalign/nucl5.fa
Tests/codonalign/pro1.aln
Tests/codonalign/pro2.aln
Tests/codonalign/pro3.aln
Tests/codonalign/pro4.aln
Tests/codonalign/pro5.aln
Tests/motifs/Arnt.sites
Tests/motifs/MA0056.1.transfac
Tests/motifs/REB1.pfm
Tests/motifs/SRF.pfm
Tests/motifs/abdb.xms
Tests/motifs/alignace.out
Tests/motifs/clusterbuster.pfm
Tests/motifs/clusterbuster.pfm.out
Tests/motifs/fourcolumns.pfm
Tests/motifs/fourrows.pfm
Tests/motifs/mast.Klf1-200.cd.oops.xml.txt
Tests/motifs/mast.Klf1-200.cd.oops.xml.xml
Tests/motifs/mast.adh.de.oops.html.txt
Tests/motifs/mast.adh.de.oops.html.xml
Tests/motifs/mast.crp0.de.oops.txt.txt
Tests/motifs/mast.crp0.de.oops.txt.xml
Tests/motifs/meme.INO_up800.classic.oops.xml
Tests/motifs/meme.adh.classic.oops.xml
Tests/motifs/meme.farntrans5.classic.anr.xml
Tests/motifs/meme.out
Tests/motifs/meme.psp_test.classic.zoops.xml
Tests/motifs/minimal_test.meme
Tests/motifs/transfac.dat
Tests/msf/DOA_prot.msf
Tests/msf/W_prot.msf
Tests/phenotype/BadPlate.json
Tests/phenotype/Plate.json
Tests/phenotype/Plate_2.json
Tests/phenotype/Plates.csv
Tests/phenotype/SmallPlate.json
Tests/phenotype/SmallPlate_2.json
Tests/phenotype/SmallPlates.csv
biopython.egg-info/PKG-INFO
biopython.egg-info/SOURCES.txt
biopython.egg-info/dependency_links.txt
biopython.egg-info/requires.txt
biopython.egg-info/top_level.txt