COPYING
MANIFEST.in
README
setup.py
nesoni/CHANGES
nesoni/__init__.py
nesoni/__main__.py
nesoni/annotation.py
nesoni/annotation_tools.py
nesoni/bio.py
nesoni/bowtie.py
nesoni/changes.py
nesoni/clip.py
nesoni/config.py
nesoni/consensus.py
nesoni/consequences.py
nesoni/core.py
nesoni/fill_scaffolds.py
nesoni/fisher_diff.py
nesoni/grace.py
nesoni/graph_layout.py
nesoni/igv.py
nesoni/io.py
nesoni/kmer.py
nesoni/legion.py
nesoni/nway_diff.py
nesoni/pastiche.py
nesoni/peaks.py
nesoni/recombination.py
nesoni/reference_directory.py
nesoni/reporting.py
nesoni/runr.py
nesoni/sam.py
nesoni/samconsensus.py
nesoni/samcount.py
nesoni/samimport.py
nesoni/samshrimp.py
nesoni/selection.py
nesoni/shred.py
nesoni/shrimp.py
nesoni/span_index.py
nesoni/statistics.py
nesoni/trivia.py
nesoni/variant.py
nesoni/workflows.py
nesoni/working_directory.py
nesoni/workspace.py
nesoni.egg-info/PKG-INFO
nesoni.egg-info/SOURCES.txt
nesoni.egg-info/dependency_links.txt
nesoni.egg-info/entry_points.txt
nesoni.egg-info/top_level.txt
nesoni/nesoni-r/DESCRIPTION
nesoni/nesoni-r/R/basic.R
nesoni/nesoni-r/R/compare.R
nesoni/nesoni-r/R/counts.R
nesoni/nesoni-r/R/io.R
nesoni/nesoni-r/R/nesoni_version.R
nesoni/nesoni-r/R/nmf.R
nesoni/nesoni-r/R/plotting.R
nesoni/third_party/__init__.py
nesoni/third_party/vcf/__init__.py
nesoni/third_party/vcf/cparse.pyx
nesoni/third_party/vcf/filters.py
nesoni/third_party/vcf/model.py
nesoni/third_party/vcf/parser.py
nesoni/third_party/vcf/utils.py
nesoni/third_party/vcf/test/__init__.py
nesoni/third_party/vcf/test/prof.py
nesoni/third_party/vcf/test/test_vcf.py
test/modify_sequence.py
test/test_analyse_samples.py
test/test_kmer.py
test/test_legion.py
test/test_nesoni.py
test/test_nesoni_consensus.py
test/test_that_treemaker_is_fast.py
test/test_that_treemaker_works.py
test/data/NC_001422-malformed.gbk
test/data/NC_001422.fna
test/data/NC_001422.gbk
test/data/NC_001422_modified.fna
test/data/NC_001422_modified.gbk
test/data/phi.fa
test/data/phihalf.fa
test/data/phiphi.fa
test/data/reads_1.txt.gz
test/data/reads_2.txt.gz
test/data/test.fa
test/data/test2.fa.bz2
test/data/test_adaptors.fa
test/data/velvet_test_reads.fa
test/data/velvet_test_reference.fa
test/data/velvet_test_reference_modified.fa
treemaker/__init__.py
treemaker/stores.py