LICENSE
MANIFEST.in
README.md
requirements.txt
setup.cfg
setup.py
setup_helper.py
versioneer.py
jcvi/__init__.py
jcvi/_version.py
jcvi.egg-info/PKG-INFO
jcvi.egg-info/SOURCES.txt
jcvi.egg-info/dependency_links.txt
jcvi.egg-info/not-zip-safe
jcvi.egg-info/requires.txt
jcvi.egg-info/top_level.txt
jcvi/algorithms/__init__.py
jcvi/algorithms/__main__.py
jcvi/algorithms/ec.py
jcvi/algorithms/formula.py
jcvi/algorithms/graph.py
jcvi/algorithms/lis.py
jcvi/algorithms/lpsolve.py
jcvi/algorithms/matrix.py
jcvi/algorithms/maxsum.py
jcvi/algorithms/ml.py
jcvi/algorithms/supermap.py
jcvi/algorithms/tsp.py
jcvi/annotation/__init__.py
jcvi/annotation/__main__.py
jcvi/annotation/ahrd.py
jcvi/annotation/automaton.py
jcvi/annotation/depth.py
jcvi/annotation/evm.py
jcvi/annotation/maker.py
jcvi/annotation/pasa.py
jcvi/annotation/qc.py
jcvi/annotation/reformat.py
jcvi/annotation/stats.py
jcvi/annotation/train.py
jcvi/apps/__init__.py
jcvi/apps/__main__.py
jcvi/apps/align.py
jcvi/apps/base.py
jcvi/apps/biomart.py
jcvi/apps/blastplus.py
jcvi/apps/bowtie.py
jcvi/apps/bwa.py
jcvi/apps/cdhit.py
jcvi/apps/emboss.py
jcvi/apps/fetch.py
jcvi/apps/gbsubmit.py
jcvi/apps/gmap.py
jcvi/apps/grid.py
jcvi/apps/ks.py
jcvi/apps/lastz.py
jcvi/apps/mask.py
jcvi/apps/phylo.py
jcvi/apps/r.py
jcvi/apps/restriction.py
jcvi/apps/script.py
jcvi/apps/softlink.py
jcvi/apps/uclust.py
jcvi/apps/uniprot.py
jcvi/apps/vecscreen.py
jcvi/assembly/__init__.py
jcvi/assembly/__main__.py
jcvi/assembly/allmaps.py
jcvi/assembly/allpaths.py
jcvi/assembly/automaton.py
jcvi/assembly/base.py
jcvi/assembly/ca.py
jcvi/assembly/chic.pyx
jcvi/assembly/coverage.py
jcvi/assembly/gaps.py
jcvi/assembly/geneticmap.py
jcvi/assembly/goldenpath.py
jcvi/assembly/hic.py
jcvi/assembly/kmer.py
jcvi/assembly/opticalmap.py
jcvi/assembly/patch.py
jcvi/assembly/postprocess.py
jcvi/assembly/preprocess.py
jcvi/assembly/sim.py
jcvi/assembly/soap.py
jcvi/assembly/syntenypath.py
jcvi/assembly/trinity.py
jcvi/compara/__init__.py
jcvi/compara/__main__.py
jcvi/compara/blastfilter.py
jcvi/compara/catalog.py
jcvi/compara/fractionation.py
jcvi/compara/pad.py
jcvi/compara/phylogeny.py
jcvi/compara/quota.py
jcvi/compara/reconstruct.py
jcvi/compara/synfind.py
jcvi/compara/synteny.py
jcvi/formats/__init__.py
jcvi/formats/__main__.py
jcvi/formats/agp.py
jcvi/formats/base.py
jcvi/formats/bed.py
jcvi/formats/blast.py
jcvi/formats/cblast.pyx
jcvi/formats/cdt.py
jcvi/formats/chain.py
jcvi/formats/contig.py
jcvi/formats/coords.py
jcvi/formats/excel.py
jcvi/formats/fasta.py
jcvi/formats/fastq.py
jcvi/formats/genbank.py
jcvi/formats/gff.py
jcvi/formats/html.py
jcvi/formats/maf.py
jcvi/formats/obo.py
jcvi/formats/paf.py
jcvi/formats/pdf.py
jcvi/formats/psl.py
jcvi/formats/pyblast.py
jcvi/formats/sam.py
jcvi/formats/sizes.py
jcvi/formats/vcf.py
jcvi/graphics/__init__.py
jcvi/graphics/__main__.py
jcvi/graphics/align.py
jcvi/graphics/assembly.py
jcvi/graphics/base.py
jcvi/graphics/blastplot.py
jcvi/graphics/chromosome.py
jcvi/graphics/coverage.py
jcvi/graphics/dotplot.py
jcvi/graphics/glyph.py
jcvi/graphics/grabseeds.py
jcvi/graphics/graph.py
jcvi/graphics/heatmap.py
jcvi/graphics/histogram.py
jcvi/graphics/karyotype.py
jcvi/graphics/landscape.py
jcvi/graphics/logo.py
jcvi/graphics/mummerplot.py
jcvi/graphics/synteny.py
jcvi/graphics/table.py
jcvi/graphics/tree.py
jcvi/graphics/wheel.py
jcvi/graphics/whisker.py
jcvi/projects/__init__.py
jcvi/projects/__main__.py
jcvi/projects/age.py
jcvi/projects/alfalfa.py
jcvi/projects/allmaps.py
jcvi/projects/bites.py
jcvi/projects/heterosis.py
jcvi/projects/ies.py
jcvi/projects/misc.py
jcvi/projects/napus.py
jcvi/projects/pineapple.py
jcvi/projects/pistachio.py
jcvi/projects/str.py
jcvi/projects/sugarcane.py
jcvi/projects/synfind.py
jcvi/projects/tgbs.py
jcvi/projects/vanilla.py
jcvi/utils/__init__.py
jcvi/utils/__main__.py
jcvi/utils/aws.py
jcvi/utils/cbook.py
jcvi/utils/console.py
jcvi/utils/db.py
jcvi/utils/ez_setup.py
jcvi/utils/grouper.py
jcvi/utils/orderedcollections.py
jcvi/utils/range.py
jcvi/utils/table.py
jcvi/utils/taxonomy.py
jcvi/utils/validator.py
jcvi/utils/webcolors.py
jcvi/utils/data/Airswing.ttf
jcvi/utils/data/Collegia.ttf
jcvi/utils/data/HookedUp.ttf
jcvi/utils/data/Humor-Sans.ttf
jcvi/utils/data/TREDs.meta.csv
jcvi/utils/data/__init__.py
jcvi/utils/data/adapters.fasta
jcvi/utils/data/blosum80.mat
jcvi/utils/data/chrY.hg38.unique_ccn.gc
jcvi/utils/data/colorchecker.txt
jcvi/utils/data/hg38.band.txt
jcvi/utils/data/hg38.chrom.sizes
jcvi/utils/data/instance.json
jcvi/variation/__init__.py
jcvi/variation/__main__.py
jcvi/variation/cnv.py
jcvi/variation/deconvolute.py
jcvi/variation/delly.py
jcvi/variation/impute.py
jcvi/variation/phase.py
jcvi/variation/snp.py
jcvi/variation/str.py
jcvi/variation/tassel.py