INSTALL
KNOWN_BUGS
LICENSE
MANIFEST.in
README.rst
README.txt
THANKS.txt
install_requisites.sh
setup.py
CGAT/AGP.py
CGAT/AString.py
CGAT/AlignedPairs.py
CGAT/Bed.py
CGAT/Bioprospector.py
CGAT/BlastAlignments.py
CGAT/Blat.py
CGAT/BlatTest.py
CGAT/CBioPortal.py
CGAT/CSV.py
CGAT/CSV2DB.py
CGAT/Cluster.py
CGAT/CorrespondenceAnalysis.py
CGAT/Database.py
CGAT/Exons.py
CGAT/Experiment.py
CGAT/Expression.py
CGAT/ExternalList.py
CGAT/Fasta.py
CGAT/FastaIterator.py
CGAT/Fastq.py
CGAT/GDLDraw.py
CGAT/GO.py
CGAT/GTF.py
CGAT/GenomicIO.py
CGAT/Genomics.py
CGAT/Glam2.py
CGAT/Glam2Scan.py
CGAT/GraphTools.py
CGAT/Histogram.py
CGAT/Histogram2D.py
CGAT/IGV.py
CGAT/IOTools.py
CGAT/IndexedFasta.py
CGAT/IndexedGenome.py
CGAT/Intervalls.py
CGAT/IntervallsWeighted.py
CGAT/Intervals.py
CGAT/Iterators.py
CGAT/Local.py
CGAT/Logfile.py
CGAT/MAST.py
CGAT/Mali.py
CGAT/MaliIO.py
CGAT/Maq.py
CGAT/Masker.py
CGAT/MatlabTools.py
CGAT/MatrixTools.py
CGAT/Metaphlan.py
CGAT/Motifs.py
CGAT/Nucmer.py
CGAT/Orthologs.py
CGAT/PamMatrices.py
CGAT/Pipeline.py
CGAT/Prediction.py
CGAT/PredictionFile.py
CGAT/PredictionParser.py
CGAT/Predictor.py
CGAT/ProfileLibrary.py
CGAT/ProfileLibraryCompass.py
CGAT/ProgressBar.py
CGAT/RLE.py
CGAT/RateEstimation.py
CGAT/Regions.py
CGAT/SVGDuplicationsWheel.py
CGAT/SVGTree.py
CGAT/SVGdraw.py
CGAT/SaryFasta.py
CGAT/SequencePairProperties.py
CGAT/SequenceProperties.py
CGAT/SetTools.py
CGAT/Sockets.py
CGAT/Stats.py
CGAT/SuffixArray.py
CGAT/Synteny.py
CGAT/Tophat.py
CGAT/Tree.py
CGAT/TreeTools.py
CGAT/VCF.py
CGAT/Variants.py
CGAT/Wiggle.py
CGAT/WrapperAdaptiveCAI.py
CGAT/WrapperBaseML.py
CGAT/WrapperBl2Seq.py
CGAT/WrapperBlastZ.py
CGAT/WrapperClustal.py
CGAT/WrapperCodeML.py
CGAT/WrapperDBA.py
CGAT/WrapperDialign.py
CGAT/WrapperENC.py
CGAT/WrapperExonerate.py
CGAT/WrapperGblocks.py
CGAT/WrapperHmmer.py
CGAT/WrapperIDR.py
CGAT/WrapperMACS.py
CGAT/WrapperMEDIPS.py
CGAT/WrapperMuscle.py
CGAT/WrapperNJTree.py
CGAT/WrapperPhylip.py
CGAT/WrapperSPP.py
CGAT/WrapperSlr.py
CGAT/WrapperZinba.py
CGAT/__init__.py
CGAT/dictzip.py
CGAT.egg-info/PKG-INFO
CGAT.egg-info/SOURCES.txt
CGAT.egg-info/dependency_links.txt
CGAT.egg-info/entry_points.txt
CGAT.egg-info/not-zip-safe
CGAT.egg-info/requires.txt
CGAT.egg-info/top_level.txt
CGAT/Components/Components.cpp
CGAT/Components/Components.pyx
CGAT/Components/connected_components.cpp
CGAT/Components/connected_components.h
CGAT/NCL/__init__.py
CGAT/NCL/_cnestedlist.pxd
CGAT/NCL/cnestedlist.pyx
CGAT/NCL/default.h
CGAT/NCL/intervaldb.c
CGAT/NCL/intervaldb.h
CGAT/Nubiscan/__init__.py
CGAT/Nubiscan/cnubiscan.pyx
scripts/_bam2bam.pyx
scripts/_bam2bam.pyxbld
scripts/_bam2bed.pyx
scripts/_bam2bed.pyxbld
scripts/_bam2geneprofile.pyx
scripts/_bam2geneprofile.pyxbld
scripts/_bam2peakshape.pyx
scripts/_bam2peakshape.pyxbld
scripts/_bam2stats.pyx
scripts/_bam2stats.pyxbld
scripts/_gtf2table.pyx
scripts/_gtf2table.pyxbld
scripts/_rnaseq_bams2bam.pyx
scripts/_rnaseq_bams2bam.pyxbld
scripts/add_random_reads_to_bam.py
scripts/add_script_template.py
scripts/align_all_vs_all.py
scripts/align_mali_vs_mali.py
scripts/align_pairs.py
scripts/align_transcripts.py
scripts/analyze_codonbias_orthology.py
scripts/analyze_go.py
scripts/analyze_readpositions.py
scripts/analyze_sequences.py
scripts/annotator2tsv.py
scripts/annotator_distance.py
scripts/bam2UniquePairs.py
scripts/bam2bam.py
scripts/bam2bed.py
scripts/bam2bidirectionaltranscription.py
scripts/bam2fastq.py
scripts/bam2geneprofile.py
scripts/bam2peakshape.py
scripts/bam2species_map.py
scripts/bam2stats.py
scripts/bam2transcriptContribution.py
scripts/bam2wiggle.py
scripts/bams2correlation.py
scripts/barplotGo.py
scripts/bed2annotator.py
scripts/bed2bed.py
scripts/bed2fasta.py
scripts/bed2gff.py
scripts/bed2graph.py
scripts/bed2plot.py
scripts/bed2psl.py
scripts/bed2stats.py
scripts/bed2table.py
scripts/beds2beds.py
scripts/beds2counts.py
scripts/blast2fasta.py
scripts/blast2table.py
scripts/calculate_histogram.py
scripts/calculate_histogram_2D.py
scripts/cat_tables.py
scripts/cgat.py
scripts/cgat2rdf.py
scripts/cgat_build_report_page.py
scripts/cgat_cluster_distribute.py
scripts/cgat_galaxy_wrapper.py
scripts/cgat_html_add_toc.py
scripts/cgat_import_extensions.py
scripts/cgat_log2wiki.py
scripts/cgat_logfiles2tsv.py
scripts/cgat_make2help.py
scripts/cgat_rebuild_extensions.py
scripts/cgat_ruffus_profile.py
scripts/cgat_script_template.py
scripts/chain2psl.py
scripts/chain2stats.py
scripts/check_db.py
scripts/clean.py
scripts/codeml2tsv.py
scripts/codemls2tsv.py
scripts/codonbias_acai2tsv.py
scripts/codonbias_shuffle_fasta.py
scripts/codonbias_weights2tsv.py
scripts/combine_gff.py
scripts/combine_histograms.py
scripts/combine_tables.py
scripts/compare_clusters.py
scripts/compare_histograms.py
scripts/contigs2random_sample.py
scripts/convert_time2seconds.py
scripts/correlate_fasta_identifier.py
scripts/coverage2stats.py
scripts/csv2csv.py
scripts/csv2db.py
scripts/csv2xls.py
scripts/csv_cut.py
scripts/csv_intersection.py
scripts/csv_rename.py
scripts/csv_set.py
scripts/csv_uniq.py
scripts/csvs2csv.py
scripts/data2bins.py
scripts/data2histogram.py
scripts/data2multiple_anova.py
scripts/data2phylocontrasts.py
scripts/data2roc.py
scripts/data2stats.py
scripts/diff_bed.py
scripts/diff_chains.py
scripts/diff_fasta.py
scripts/diff_gtf.py
scripts/diff_gtfs.py
scripts/diff_transcript_sets.py
scripts/ena2table.py
scripts/extractseq.py
scripts/farm.py
scripts/fasta2bed.py
scripts/fasta2counts.py
scripts/fasta2distances.py
scripts/fasta2fasta.py
scripts/fasta2gff.py
scripts/fasta2kmercontent.py
scripts/fasta2nj.py
scripts/fasta2table.py
scripts/fasta2variants.py
scripts/fastas2fasta.py
scripts/fastq2N.py
scripts/fastq2fastq.py
scripts/fastq2solid.py
scripts/fastq2table.py
scripts/fastqs2fasta.py
scripts/fastqs2fastq.py
scripts/filter_reads.py
scripts/filter_tokens.py
scripts/formatMetagenemark.py
scripts/genelist_analysis.py
scripts/genome_bed.py
scripts/geo2table.py
scripts/gff2annotator.py
scripts/gff2bed.py
scripts/gff2coverage.py
scripts/gff2fasta.py
scripts/gff2gff.py
scripts/gff2histogram.py
scripts/gff2plot.py
scripts/gff2psl.py
scripts/gff2stats.py
scripts/gff2table.py
scripts/gff2view.py
scripts/gff_compare.py
scripts/gff_decorate.py
scripts/gff_ensembl2gbrowser.py
scripts/go2plot.py
scripts/go2svg.py
scripts/graph2besthits.py
scripts/graph2stats.py
scripts/graph_blast2besthits.py
scripts/graph_blast2pairs.py
scripts/graph_check.py
scripts/graph_check_transitivity.py
scripts/graph_cluster_by_species.py
scripts/graph_combine_links_redundant.py
scripts/graph_filter_links_redundant.py
scripts/graph_group_links_by_taxonomy.py
scripts/graph_links2gdl.py
scripts/graph_map_links.py
scripts/graph_reweight_links.py
scripts/gtf2alleles.py
scripts/gtf2fasta.py
scripts/gtf2gff.py
scripts/gtf2gtf.py
scripts/gtf2overlap.py
scripts/gtf2reads.py
scripts/gtf2table.py
scripts/gtf2tsv.py
scripts/gtfs2graph.py
scripts/histogram2histogram.py
scripts/histograms2kl.py
scripts/index2bed.py
scripts/index2gff.py
scripts/index_fasta.py
scripts/intervaltable2bed.py
scripts/introns2rates.py
scripts/jalview.py
scripts/join_tables.py
scripts/liftover.py
scripts/links2fasta.py
scripts/list_overlap.py
scripts/maf2psl.py
scripts/mali2bootstrap.py
scripts/mali2cleaned_mali.py
scripts/mali2kaks.py
scripts/mali2mali.py
scripts/mali2malis.py
scripts/mali2predictions.py
scripts/mali2rates.py
scripts/mali2summary.py
scripts/mali2table.py
scripts/mali_evaluate.py
scripts/mali_extract.py
scripts/mali_phylip2fasta.py
scripts/mali_plain2aln.py
scripts/mali_remove_gaps.py
scripts/malis2mali.py
scripts/malis2malis.py
scripts/malis2masks.py
scripts/malis2profiles.py
scripts/map_residues.py
scripts/maq2assembly.py
scripts/maq2psl.py
scripts/mask_fasta.py
scripts/matrix2matrix.py
scripts/matrix2stats.py
scripts/matrix2tree.py
scripts/medip_merge_intervals.py
scripts/merge_tables.py
scripts/modify_table.py
scripts/mysql_clone_database.py
scripts/mysql_copy_tables.py
scripts/nmf.py
scripts/nofarm.py
scripts/nr2table.py
scripts/nucmer2bed.py
scripts/numbers2rgb.py
scripts/peptides2cds.py
scripts/plot_data.py
scripts/plot_histogram.py
scripts/plot_matrix.py
scripts/png2svg.py
scripts/probeset2gene.py
scripts/psl2assembly.py
scripts/psl2chain.py
scripts/psl2fasta.py
scripts/psl2gff.py
scripts/psl2map.py
scripts/psl2predictions.py
scripts/psl2psl.py
scripts/psl2stats.py
scripts/psl2table.py
scripts/psl2wiggle.py
scripts/psl2wiggle_stats.py
scripts/psql_add_tables.py
scripts/psql_clone_database.py
scripts/qkill.py
scripts/quality2fasta.py
scripts/quality2masks.py
scripts/r_compare_distributions.py
scripts/r_mann_whitney_u.py
scripts/r_table2scatter.py
scripts/r_test.py
scripts/radar.py
scripts/rates2rates.py
scripts/rename_links.py
scripts/revigo.py
scripts/rnaseq_bam_vs_bed.py
scripts/rnaseq_bam_vs_exons.py
scripts/rnaseq_bams2bam.py
scripts/rnaseq_bams_vs_bams.py
scripts/rnaseq_junction_bam2bam.py
scripts/run.py
scripts/runExpression.py
scripts/runGO.py
scripts/run_function.py
scripts/run_nubiscan.py
scripts/sequence2alignment.py
scripts/sequences2graph.py
scripts/sequences2mali.py
scripts/set_diff.py
scripts/simulate_function.py
scripts/snp2counts.py
scripts/snp2maf.py
scripts/snp2snp.py
scripts/snp2table.py
scripts/softmask.py
scripts/solexa2stats.py
scripts/sparse2full.py
scripts/species_map2species_map.py
scripts/split_fasta.py
scripts/split_file.py
scripts/split_genome.py
scripts/split_genomic_fasta_file.py
scripts/split_gff.py
scripts/split_links.py
scripts/submit.py
scripts/substitute_tokens.py
scripts/table2graph.py
scripts/table2table.py
scripts/tree2matrix.py
scripts/tree2patterns.py
scripts/tree2plot.py
scripts/tree2stats.py
scripts/tree2svg.py
scripts/tree2taxa.py
scripts/tree2tree.py
scripts/tree_collapse_species.py
scripts/tree_diff.py
scripts/tree_map_leaves.py
scripts/tree_species2genes.py
scripts/tree_strain2species.py
scripts/trees2sets.py
scripts/trees2tree.py
scripts/trees2trees.py
scripts/vcf2vcf.py
scripts/vcfstats2db.py
scripts/wig2bed.py
scripts/wig2wig.py
scripts/wiggle_build_index.py
scripts/wiggle_extract_ranges_indexed.py