.gitignore
.pre-commit-config.yaml
LICENSE
MANIFEST.in
README.md
pyproject.toml
requirements-live.txt
requirements.txt
.github/workflows/deploy.yml
.github/workflows/test.yml
samples/Taxi2test1_10.tab
samples/Taxi2test1_120.tab
samples/Taxi2test1_50.tab
samples/Taxi2test1_ca1000.tab
samples/Taxi2test1_ca200.tab
samples/Taxi2test1_ca2000.tab
samples/Taxi2test1_ca500.tab
samples/Taxi2test1_ca9000.tab
samples/ingroup.tab
samples/input.tab
samples/outgroup.tab
scripts/decontaminate.py
scripts/decontaminate2.py
scripts/dereplicate.py
scripts/versusAll.py
scripts/versusReference.py
src/itaxotools/taxi2/__init__.py
src/itaxotools/taxi2/align.py
src/itaxotools/taxi2/distances.py
src/itaxotools/taxi2/encoding.py
src/itaxotools/taxi2/file_types.py
src/itaxotools/taxi2/files.py
src/itaxotools/taxi2/handlers.py
src/itaxotools/taxi2/pairs.py
src/itaxotools/taxi2/partitions.py
src/itaxotools/taxi2/plot.py
src/itaxotools/taxi2/sequences.py
src/itaxotools/taxi2/statistics.py
src/itaxotools/taxi2/trees.py
src/itaxotools/taxi2/types.py
src/itaxotools/taxi2/tasks/__init__.py
src/itaxotools/taxi2/tasks/decontaminate.py
src/itaxotools/taxi2/tasks/decontaminate2.py
src/itaxotools/taxi2/tasks/dereplicate.py
src/itaxotools/taxi2/tasks/versus_all.py
src/itaxotools/taxi2/tasks/versus_reference.py
src/itaxotools_taxi2.egg-info/PKG-INFO
src/itaxotools_taxi2.egg-info/SOURCES.txt
src/itaxotools_taxi2.egg-info/dependency_links.txt
src/itaxotools_taxi2.egg-info/entry_points.txt
src/itaxotools_taxi2.egg-info/requires.txt
src/itaxotools_taxi2.egg-info/top_level.txt
tests/test_align.py
tests/test_distances.py
tests/test_files.py
tests/test_handlers.py
tests/test_new_versus_reference.py
tests/test_pairs.py
tests/test_partitions.py
tests/test_sequences.py
tests/test_statistics.py
tests/test_trees.py
tests/test_types.py
tests/utility.py
tests/test_distances/empty
tests/test_distances/extras.tsv
tests/test_distances/metrics.tsv
tests/test_distances/missing.formatted.linear
tests/test_distances/missing.formatted.matrix
tests/test_distances/missing.linear
tests/test_distances/missing.matrix
tests/test_distances/multiple.linear
tests/test_distances/rectangle.matrix
tests/test_distances/simple.linear
tests/test_distances/square.matrix
tests/test_files/binomen.tsv
tests/test_files/complex.tree
tests/test_files/empty.txt
tests/test_files/full.tsv
tests/test_files/simple.fasta
tests/test_files/simple.spart
tests/test_files/simple.tree
tests/test_files/simple.tsv
tests/test_files/simple.xml
tests/test_files/spaces.fasta
tests/test_files/species.dot.fasta
tests/test_files/species.fasta
tests/test_handlers/empty.tsv
tests/test_handlers/headers.tsv
tests/test_handlers/headers.xlsx
tests/test_handlers/simple.tsv
tests/test_handlers/simple.xlsx
tests/test_new_versus_reference/simple.output.tsv
tests/test_new_versus_reference/simple.query.tsv
tests/test_new_versus_reference/simple.ref.tsv
tests/test_pairs/simple.formatted
tests/test_pairs/simple.tsv
tests/test_partitions/extras.tsv
tests/test_partitions/genera.fas
tests/test_partitions/genera.tsv
tests/test_partitions/missing.fas
tests/test_partitions/simple.dot.fas
tests/test_partitions/simple.fas
tests/test_partitions/simple.spart
tests/test_partitions/simple.tsv
tests/test_partitions/simple.xml
tests/test_sequences/alleles.concat.fas
tests/test_sequences/alleles.plain.fas
tests/test_sequences/alleles.species.fas
tests/test_sequences/empty
tests/test_sequences/empty.tsv
tests/test_sequences/headers.tsv
tests/test_sequences/headers.xlsx
tests/test_sequences/quality.fq
tests/test_sequences/simple.ali
tests/test_sequences/simple.fas
tests/test_sequences/simple.gbk
tests/test_sequences/simple.multi.fas
tests/test_sequences/simple.tsv
tests/test_sequences/simple.width.fas
tests/test_sequences/simple.xlsx
tests/test_sequences/species.dot.fas
tests/test_sequences/species.fas
tests/test_statistics/percent.groups
tests/test_statistics/percent.single
tests/test_statistics/simple.groups
tests/test_statistics/simple.single
tests/test_statistics/tiny.groups
tests/test_statistics/tiny.single
tests/test_trees/bad.tree
tests/test_trees/complex.tree
tests/test_trees/multiple.tree
tests/test_trees/single.tree