.gitattributes
.gitignore
.pre-commit-config.yaml
AGENTS.md
CONTRIBUTING.md
Dockerfile
LICENSE
MANIFEST.in
README.md
README.rst
README.rst2
RELEASING.md
code_review.md
replidec_banner.jpg
requirements-dev.txt
requirements.txt
setup.cfg
setup.py
.conda/meta.yaml
.github/CODEOWNERS
.github/ISSUE_TEMPLATE.md
.github/pull_request_template.md
.github/workflows/release.yml
.github/workflows/test.yml
Replidec/Replidec.py
Replidec/Replidec_cmdline.py
Replidec/Replidec_multi.py
Replidec/__init__.py
Replidec/utility.py
Replidec.egg-info/PKG-INFO
Replidec.egg-info/SOURCES.txt
Replidec.egg-info/dependency_links.txt
Replidec.egg-info/entry_points.txt
Replidec.egg-info/requires.txt
Replidec.egg-info/top_level.txt
Replidec.egg-info/zip-safe
scripts/check_release_version.py
scripts/update_bioconda_recipe.py
test/example.sh
test/test_release_tools.py
test/example/example.list
test/example/example.small.list
test/example/genome_test.index
test/example/genome_test.small.index
test/example/mock_data_single_lifestyleBC.py
test/example/simulate_art_sample1.1.faa
test/example/simulate_art_sample1.10.faa
test/example/simulate_art_sample1.11.faa
test/example/simulate_art_sample1.12.faa
test/example/simulate_art_sample1.13.faa
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test/example/simulate_art_sample1.16.faa
test/example/simulate_art_sample1.17.faa
test/example/simulate_art_sample1.18.faa
test/example/simulate_art_sample1.19.faa
test/example/simulate_art_sample1.2.faa
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test/example/simulate_art_sample1.22.faa
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test/example/simulate_art_sample1.4.faa
test/example/simulate_art_sample1.5.faa
test/example/simulate_art_sample1.6.faa
test/example/simulate_art_sample1.7.faa
test/example/simulate_art_sample1.8.faa
test/example/simulate_art_sample1.9.faa
test/example/test.contig.small.fa
test/example/test.contig.small.new.fa
test/example/genome_test/generate.sh
test/example/genome_test/genome.test.fnaaa
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test/example/genome_test/genome.test.fnaac
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