LICENSE
MANIFEST.in
README.md
requirements.txt
setup.py
setup_helper.py
./__init__.py
./__main__.py
./setup_helper.py
./tests.py
./algorithms/__init__.py
./algorithms/__main__.py
./algorithms/ec.py
./algorithms/formula.py
./algorithms/graph.py
./algorithms/lis.py
./algorithms/lpsolve.py
./algorithms/matrix.py
./algorithms/maxsum.py
./algorithms/ml.py
./algorithms/supermap.py
./algorithms/tsp.py
./annotation/__init__.py
./annotation/__main__.py
./annotation/ahrd.py
./annotation/automaton.py
./annotation/depth.py
./annotation/evm.py
./annotation/maker.py
./annotation/pasa.py
./annotation/qc.py
./annotation/reformat.py
./annotation/stats.py
./annotation/train.py
./apps/__init__.py
./apps/__main__.py
./apps/align.py
./apps/base.py
./apps/biomart.py
./apps/blastplus.py
./apps/bowtie.py
./apps/bwa.py
./apps/cap3.py
./apps/cdhit.py
./apps/console.py
./apps/emboss.py
./apps/fetch.py
./apps/gbsubmit.py
./apps/gmap.py
./apps/grid.py
./apps/ks.py
./apps/lastz.py
./apps/mask.py
./apps/phylo.py
./apps/r.py
./apps/restriction.py
./apps/script.py
./apps/softlink.py
./apps/tesseract.py
./apps/uclust.py
./apps/uniprot.py
./apps/vecscreen.py
./assembly/__init__.py
./assembly/__main__.py
./assembly/allmaps.py
./assembly/allpaths.py
./assembly/amos.py
./assembly/automaton.py
./assembly/bambus.py
./assembly/base.py
./assembly/ca.py
./assembly/coverage.py
./assembly/gaps.py
./assembly/geneticmap.py
./assembly/goldenpath.py
./assembly/hic.py
./assembly/kmer.py
./assembly/meraculous.py
./assembly/opticalmap.py
./assembly/patch.py
./assembly/pbjelly.py
./assembly/postprocess.py
./assembly/preprocess.py
./assembly/sim.py
./assembly/soap.py
./assembly/sspace.py
./assembly/syntenypath.py
./assembly/trinity.py
./assembly/unitig.py
./compara/__init__.py
./compara/__main__.py
./compara/blastfilter.py
./compara/catalog.py
./compara/fractionation.py
./compara/pad.py
./compara/quota.py
./compara/reconstruct.py
./compara/synfind.py
./compara/synteny.py
./formats/__init__.py
./formats/__main__.py
./formats/ace.py
./formats/agp.py
./formats/base.py
./formats/bed.py
./formats/blast.py
./formats/btab.py
./formats/cdt.py
./formats/chain.py
./formats/contig.py
./formats/coords.py
./formats/excel.py
./formats/fasta.py
./formats/fastq.py
./formats/fpc.py
./formats/genbank.py
./formats/gff.py
./formats/html.py
./formats/maf.py
./formats/obo.py
./formats/pdf.py
./formats/posmap.py
./formats/psl.py
./formats/sam.py
./formats/sbt.py
./formats/sizes.py
./formats/vcf.py
./graphics/__init__.py
./graphics/__main__.py
./graphics/align.py
./graphics/assembly.py
./graphics/base.py
./graphics/blastplot.py
./graphics/chromosome.py
./graphics/coverage.py
./graphics/dotplot.py
./graphics/glyph.py
./graphics/grabseeds.py
./graphics/graph.py
./graphics/heatmap.py
./graphics/histogram.py
./graphics/karyotype.py
./graphics/landscape.py
./graphics/logo.py
./graphics/mummerplot.py
./graphics/synteny.py
./graphics/tree.py
./graphics/wheel.py
./graphics/whisker.py
./projects/__init__.py
./projects/__main__.py
./projects/age.py
./projects/alfalfa.py
./projects/allmaps.py
./projects/bites.py
./projects/heterosis.py
./projects/ies.py
./projects/misc.py
./projects/napus.py
./projects/pineapple.py
./projects/pistachio.py
./projects/str.py
./projects/synfind.py
./projects/tgbs.py
./utils/__init__.py
./utils/__main__.py
./utils/aws.py
./utils/brewer2mpl.py
./utils/cbook.py
./utils/counter.py
./utils/db.py
./utils/ez_setup.py
./utils/grouper.py
./utils/iter.py
./utils/natsort.py
./utils/orderedcollections.py
./utils/progressbar.py
./utils/range.py
./utils/table.py
./utils/taxonomy.py
./utils/webcolors.py
./utils/data/__init__.py
./variation/__init__.py
./variation/__main__.py
./variation/cnv.py
./variation/deconvolute.py
./variation/delly.py
./variation/impute.py
./variation/phase.py
./variation/snp.py
./variation/str.py
./variation/tassel.py
assembly/chic.pyx
formats/cblast.pyx
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
utils/data/Airswing.ttf
utils/data/Collegia.ttf
utils/data/HookedUp.ttf
utils/data/Humor-Sans.ttf
utils/data/TREDs.meta.csv
utils/data/__init__.py
utils/data/adapters.fasta
utils/data/blosum80.mat
utils/data/chrY.hg38.unique_ccn.gc
utils/data/colorbrewer_all_schemes.json
utils/data/colorchecker.txt
utils/data/hg38.band.txt
utils/data/hg38.chrom.sizes
utils/data/instance.json