./.codecov.yml .all-contributorsrc .flake8 CITATIONS CODEOWNERS LICENSE MANIFEST.in Makefile docs/Makefile docs/about.rst docs/api/Makefile docs/api/conf.py docs/api/index.rst docs/api/make.bat docs/api/pyani.anib.rst docs/api/pyani.aniblastall.rst docs/api/pyani.anim.rst docs/api/pyani.blast.rst docs/api/pyani.dependencies.rst docs/api/pyani.download.rst docs/api/pyani.logger.rst docs/api/pyani.nucmer.rst docs/api/pyani.pyani_classify.rst docs/api/pyani.pyani_config.rst docs/api/pyani.pyani_files.rst docs/api/pyani.pyani_graphics.mpl.rst docs/api/pyani.pyani_graphics.rst docs/api/pyani.pyani_graphics.sns.rst docs/api/pyani.pyani_jobs.rst docs/api/pyani.pyani_orm.rst docs/api/pyani.pyani_report.rst docs/api/pyani.pyani_tools.rst docs/api/pyani.rst docs/api/pyani.run_multiprocessing.rst docs/api/pyani.run_sge.rst docs/api/pyani.scripts.average_nucleotide_identity.rst docs/api/pyani.scripts.delta_filter_wrapper.rst docs/api/pyani.scripts.genbank_get_genomes_by_taxon.rst 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docs/subcmd_download.rst docs/subcmd_index.rst docs/subcmd_listdeps.rst docs/subcmd_plot.rst docs/subcmd_report.rst docs/subcommands.rst docs/testing.rst docs/using_a_scheduler.rst pyani/__init__.py pyani/anib.py pyani/aniblastall.py pyani/anim.py pyani/blast.py pyani/dependencies.py pyani/download.py pyani/logger.py pyani/nucmer.py pyani/pyani_classify.py pyani/pyani_config.py pyani/pyani_files.py pyani/pyani_graphics/__init__.py pyani/pyani_graphics/mpl/__init__.py pyani/pyani_graphics/sns/__init__.py pyani/pyani_jobs.py pyani/pyani_orm.py pyani/pyani_report.py pyani/pyani_tools.py pyani/run_multiprocessing.py pyani/run_sge.py pyani/scripts/__init__.py pyani/scripts/average_nucleotide_identity.py pyani/scripts/delta_filter_wrapper.py pyani/scripts/genbank_get_genomes_by_taxon.py pyani/scripts/parsers/__init__.py pyani/scripts/parsers/anib_parser.py pyani/scripts/parsers/aniblastall_parser.py pyani/scripts/parsers/anim_parser.py pyani/scripts/parsers/classify_parser.py 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tests/test_targets/subcmd_index/GCF_000185985.2_ASM18598v2_genomic.fna.md5 tests/test_targets/subcmd_index/GCF_000331065.1_ASM33106v1_genomic.fna.md5 tests/test_targets/subcmd_index/GCF_000973505.1_ASM97350v1_genomic.fna.md5 tests/test_targets/subcmd_index/GCF_000973545.1_ASM97354v1_genomic.fna.md5 tests/test_tetra.py tests/tools.py <<<<<< network # path=.coverage.xml /home/circleci/repo/pyani <<<<<< EOF