CONTRIB
CONTRIB.rst
CONTRIBUTING.rst
DEPRECATED
DEPRECATED.rst
LICENSE
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MANIFEST.in
NEWS
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README
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setup.cfg
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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/internal_oligo.primer3
Tests/Emboss/matcher_pair.txt
Tests/Emboss/matcher_simple.txt
Tests/Emboss/needle.txt
Tests/Emboss/needle_asis.txt
Tests/Emboss/no_oligo.primer3
Tests/Emboss/short.primer3
Tests/Emboss/water.txt
Tests/Emboss/water2.txt
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/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/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_cdna2genome.exn
Tests/Exonerate/exn_22_m_coding2coding.exn
Tests/Exonerate/exn_22_m_coding2coding_fshifts.exn
Tests/Exonerate/exn_22_m_coding2genome.exn
Tests/Exonerate/exn_22_m_dna2protein.exn
Tests/Exonerate/exn_22_m_est2genome.exn
Tests/Exonerate/exn_22_m_genome2genome.exn
Tests/Exonerate/exn_22_m_ner.exn
Tests/Exonerate/exn_22_m_protein2dna.exn
Tests/Exonerate/exn_22_m_protein2dna_fshifts.exn
Tests/Exonerate/exn_22_m_protein2genome.exn
Tests/Exonerate/exn_22_m_ungapped.exn
Tests/Exonerate/exn_22_m_ungapped_trans.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_vulgar.exn
Tests/Exonerate/exn_22_q_none.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/lavender.nu
Tests/Fasta/loveliesbleeding.pro
Tests/Fasta/lupine.nu
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/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/GenBank/1MRR_A.gp
Tests/GenBank/DS830848.gb
Tests/GenBank/EU851978.gbk
Tests/GenBank/EU851978_output.gbk
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/arab1.gb
Tests/GenBank/bad_loc_wrap.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/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/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/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
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Tests/Hmmer/tab_31b1_hmmscan_001.out
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Tests/Hmmer/text_20_hmmsearch_001.out
Tests/Hmmer/text_21_hmmpfam_001.out
Tests/Hmmer/text_22_hmmpfam_001.out
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Tests/Hmmer/text_24_hmmpfam_001.out
Tests/Hmmer/text_30_hmmscan_001.out
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Tests/Hmmer/text_30_hmmscan_006.out
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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
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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.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.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.maf
Tests/MAF/unfinished.idx
Tests/MAF/wrong_version.idx
Tests/Mauve/simple.fa
Tests/Mauve/simple.xmfa
Tests/Mauve/simple.xmfa.backbone
Tests/Mauve/simple.xmfa.bbcols
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/Motif/Arnt.sites
Tests/Motif/REB1.pfm
Tests/Motif/SRF.pfm
Tests/Motif/alignace.out
Tests/Motif/mast.dna.oops.txt
Tests/Motif/mast.protein.oops.txt
Tests/Motif/mast.protein.tcm.txt
Tests/Motif/meme.dna.oops.txt
Tests/Motif/meme.out
Tests/Motif/meme.protein.oops.txt
Tests/Motif/meme.protein.tcm.txt
Tests/Motif/transfac.dat
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/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/PAML/gen_results.py
Tests/PAML/Alignments/aa_alignment.phylip
Tests/PAML/Alignments/alignment.phylip
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_long.ctl
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Tests/PAML/Results/baseml/baseml_alpha1rho1.out
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Tests/PAML/Results/baseml/SE/SE-4_4.out
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Tests/PAML/Results/baseml/SE/SE-4_6.out
Tests/PAML/Results/baseml/SE/SE-4_7.out
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Tests/PAML/Results/baseml/alpha1rho1/alpha1rho1-4_7.out
Tests/PAML/Results/baseml/model/model0-4_1.out
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Tests/PAML/Results/baseml/model/model1-4_3.out
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Tests/PAML/Results/baseml/model/model3-4_1.out
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Tests/PAML/Results/baseml/model/model3-4_4.out
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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_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/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.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/Miller_RASA.txt
Tests/PDB/Sander_RASA.txt
Tests/PDB/Wilke_RASA.txt
Tests/PDB/a_structure.pdb
Tests/PDB/alignment_file.fa
Tests/PDB/dssp_xtra_Sander.txt
Tests/PDB/ions.pdb
Tests/PDB/lib_10_z_5.txt
Tests/PDB/occupancy.pdb
Tests/Phd/phd1
Tests/Phd/phd2
Tests/Phd/phd_454
Tests/Phd/phd_solexa
Tests/Phylip/hennigian.phy
Tests/Phylip/horses.phy
Tests/Phylip/horses.tree
Tests/Phylip/interlaced.phy
Tests/Phylip/interlaced2.phy
Tests/Phylip/random.phy
Tests/Phylip/reference_dna.phy
Tests/Phylip/reference_dna2.phy
Tests/Phylip/sequential.phy
Tests/Phylip/sequential2.phy
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/Stockholm/funny.sth
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/P84001.xml
Tests/SwissProt/P97881.xml
Tests/SwissProt/Q13639.txt
Tests/SwissProt/Q13639.xml
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/sp001
Tests/SwissProt/sp002
Tests/SwissProt/sp003
Tests/SwissProt/sp004
Tests/SwissProt/sp005
Tests/SwissProt/sp006
Tests/SwissProt/sp007
Tests/SwissProt/sp008
Tests/SwissProt/sp009
Tests/SwissProt/sp010
Tests/SwissProt/sp011
Tests/SwissProt/sp012
Tests/SwissProt/sp013
Tests/SwissProt/sp014
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/pars3.tre
Tests/TreeConstruction/strict_refs.tre
Tests/TreeConstruction/test.log
Tests/TreeConstruction/trees.tre
Tests/TreeConstruction/upgma.tre
Tests/UniGene/Eca.1.2425.data
Tests/UniGene/Hs.2.data
Tests/UniGene/Mdm_partial.data
Tests/UniProt/goa_yeast.gaf
Tests/Wise/human_114_g01_exons.fna_01
Tests/Wise/human_114_g02_exons.fna_01
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/REB1.pfm
Tests/motifs/SRF.pfm
Tests/motifs/alignace.out
Tests/motifs/mast.dna.oops.txt
Tests/motifs/mast.protein.oops.txt
Tests/motifs/mast.protein.tcm.txt
Tests/motifs/meme.dna.oops.txt
Tests/motifs/meme.out
Tests/motifs/meme.protein.oops.txt
Tests/motifs/meme.protein.tcm.txt
Tests/motifs/meme.rna.oops.txt
Tests/motifs/meme_v_4_11_4.txt
Tests/motifs/transfac.dat
Tests/output/test_AlignIO
Tests/output/test_AlignIO_MauveIO
Tests/output/test_ClustalOmega_tool
Tests/output/test_Clustalw
Tests/output/test_Clustalw_tool
Tests/output/test_CodonUsage
Tests/output/test_DocSQL
Tests/output/test_FSSP
Tests/output/test_Fasttree_tool
Tests/output/test_File
Tests/output/test_GFF
Tests/output/test_GFF2
Tests/output/test_GenBank
Tests/output/test_HMMCasino
Tests/output/test_KEGG
Tests/output/test_Location
Tests/output/test_NCBI_qblast
Tests/output/test_NNExclusiveOr
Tests/output/test_PDB
Tests/output/test_ParserSupport
Tests/output/test_SeqIO
Tests/output/test_SubsMat
Tests/output/test_align
Tests/output/test_geo
Tests/output/test_property_manager
Tests/output/test_translate
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