.gitignore
.pre-commit-config.yaml
LICENSE.txt
MANIFEST.in
README.md
pyproject.toml
requirements-live.txt
requirements.txt
.github/workflows/deploy.yml
.github/workflows/macos.yml
.github/workflows/test.yml
.github/workflows/windows.yml
examples/ConvPhase_examplefile1.tsv
examples/Convphase_examplefile1_HapViewformat_fasta.fas
examples/Convphase_examplefile1_MolDformat_fasta.fas
examples/Convphase_examplefile1_regular_fasta.fas
examples/Convphase_examplefile2.tsv
examples/Convphase_examplefile2_HapViewformat_fasta.fas
examples/Convphase_examplefile2_MolDformat_fasta.fas
examples/Convphase_examplefile2_regular_fasta.fas
examples/Hapsolutely_examplefile3_regular_fasta.fas
examples/Hapsolutely_examplefile3_regular_fasta_phased.fas
examples/Hapsolutely_examplefile3_spartitions.spart
examples/Hapsolutely_examplefile4_regular_fasta_long.fas
examples/Hapsolutely_examplefile4_regular_fasta_short.fas
examples/Hapsolutely_examplefile4_spartition.tsv
examples/Hapsolutely_examplefile4_spartitions.spart
examples/Hapsolutely_examplefile5_haploidseqs_regular_fasta.fas
examples/Hapsolutely_examplefile5_spartition.tsv
examples/cmos_mabuya/cmos_mabuya.duplicated.fas.spart
examples/cmos_mabuya/cmos_mabuya.fas
examples/cmos_mabuya/cmos_mabuya.fas.spart
examples/cmos_mabuya/cmos_mabuya.phased.fas
examples/cmos_mabuya/cmos_mabuya_named.phased.txt
examples/malagasius/malagasius.formated.fas
examples/malagasius/malagasius.phased.fas
examples/simple/phased.ab.spart
examples/simple/phased.ab.xml
examples/simple/phased.dot.fas
examples/simple/phased.fas
examples/simple/phased.plain.fas
examples/simple/phased.spart
examples/simple/phased.tree
examples/simple/phased.tsv
examples/simple/phased.xml
examples/simple/simple.fas
examples/simple/simple.tsv
images/screenshot.png
src/itaxotools/__pyinstaller/hook-itaxotools.hapsolutely.py
src/itaxotools/hapsolutely/__init__.py
src/itaxotools/hapsolutely/app.py
src/itaxotools/hapsolutely/config.py
src/itaxotools/hapsolutely/fitchi.py
src/itaxotools/hapsolutely/resources.py
src/itaxotools/hapsolutely/yamlify.py
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src/itaxotools/hapsolutely/documents/nets.html
src/itaxotools/hapsolutely/documents/phase.html
src/itaxotools/hapsolutely/graphics/about.svg
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src/itaxotools/hapsolutely/graphics/phase.svg
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src/itaxotools/hapsolutely/icons/zoom.svg
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src/itaxotools/hapsolutely/logos/hapsolutely_h.svg
src/itaxotools/hapsolutely/model/phased_results.py
src/itaxotools/hapsolutely/model/phased_sequence.py
src/itaxotools/hapsolutely/tasks/about/__init__.py
src/itaxotools/hapsolutely/tasks/about/model.py
src/itaxotools/hapsolutely/tasks/about/view.py
src/itaxotools/hapsolutely/tasks/common/model.py
src/itaxotools/hapsolutely/tasks/common/types.py
src/itaxotools/hapsolutely/tasks/common/view.py
src/itaxotools/hapsolutely/tasks/common/work.py
src/itaxotools/hapsolutely/tasks/convphase/__init__.py
src/itaxotools/hapsolutely/tasks/convphase/model.py
src/itaxotools/hapsolutely/tasks/convphase/view.py
src/itaxotools/hapsolutely/tasks/haplodemo/__init__.py
src/itaxotools/hapsolutely/tasks/haplodemo/model.py
src/itaxotools/hapsolutely/tasks/haplodemo/process.py
src/itaxotools/hapsolutely/tasks/haplodemo/types.py
src/itaxotools/hapsolutely/tasks/haplodemo/view.py
src/itaxotools/hapsolutely/tasks/haplodemo/widgets.py
src/itaxotools/hapsolutely/tasks/haplodemo/work.py
src/itaxotools/hapsolutely/tasks/haplostats/__init__.py
src/itaxotools/hapsolutely/tasks/haplostats/model.py
src/itaxotools/hapsolutely/tasks/haplostats/process.py
src/itaxotools/hapsolutely/tasks/haplostats/types.py
src/itaxotools/hapsolutely/tasks/haplostats/view.py
src/itaxotools/hapsolutely/tasks/haplostats/work.py
src/itaxotools_hapsolutely.egg-info/PKG-INFO
src/itaxotools_hapsolutely.egg-info/SOURCES.txt
src/itaxotools_hapsolutely.egg-info/dependency_links.txt
src/itaxotools_hapsolutely.egg-info/entry_points.txt
src/itaxotools_hapsolutely.egg-info/requires.txt
src/itaxotools_hapsolutely.egg-info/top_level.txt
tests/conftest.py
tests/test_main.py
tests/test_haplostats/error/duplicate_allele.fas
tests/test_haplostats/error/duplicate_allele.tsv
tests/test_haplostats/error/out_of_order_allele.fas
tests/test_haplostats/warn/multiple_allele.fas
tests/test_haplostats/warn/multiple_allele.tsv
tests/test_haplostats/warn/single_allele.fas
tests/test_haplostats/warn/single_allele.tsv
tests/test_haplostats/warn/unexpected_allele.fas
tests/test_haplostats/warn/unexpected_allele.tsv
tools/config.sh
tools/make-bundle.sh
tools/make-disk-image.sh
tools/make-executable.sh
tools/notarize.sh
tools/package.sh
tools/run.py
tools/sign.sh
tools/data/entitlements.plist
tools/data/hapsolutely.icns
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tools/specs/macos.spec
tools/specs/windows.spec
tools/wheels/install.py
tools/wheels/macos.yml