.gitignore
LICENSE.txt
README.md
TODO.md
environment.yml
pyproject.toml
zensical.toml
.github/workflows/publish-pypi.yml
conda.recipe/README.md
conda.recipe/meta.yaml
docs/index.md
docs/_templates/README.md
docs/_templates/command-reference.md
docs/_templates/concept-guide.md
docs/_templates/section-landing.md
docs/analyses/dapc.md
docs/analyses/index.md
docs/analyses/pca.md
docs/analyses/popgen.md
docs/assembly/assemble.md
docs/assembly/demux.md
docs/assembly/denovo.md
docs/assembly/index.md
docs/assembly/map.md
docs/assembly/trim.md
docs/css/notebook-markdown.css
docs/getting-started/ethos.md
docs/getting-started/files-and-data-types.md
docs/getting-started/installation.md
docs/getting-started/what-is-ipyrad.md
docs/recipes/index.md
docs/recipes/sample-name-parsing.md
docs/writing-outputs/index.md
docs/writing-outputs/lex.md
docs/writing-outputs/snpex.md
docs/writing-outputs/wex.md
ipyrad2/__init__.py
ipyrad2/_version.py
ipyrad2.egg-info/PKG-INFO
ipyrad2.egg-info/SOURCES.txt
ipyrad2.egg-info/dependency_links.txt
ipyrad2.egg-info/entry_points.txt
ipyrad2.egg-info/requires.txt
ipyrad2.egg-info/scm_file_list.json
ipyrad2.egg-info/scm_version.json
ipyrad2.egg-info/top_level.txt
ipyrad2/analysis/__init__.py
ipyrad2/analysis/utils.py
ipyrad2/analysis/converters/__init__.py
ipyrad2/analysis/converters/vcf_to_hdf5.py
ipyrad2/analysis/extracters/__init__.py
ipyrad2/analysis/extracters/locus_extracter.py
ipyrad2/analysis/extracters/sequence_common.py
ipyrad2/analysis/extracters/snps_extracter.py
ipyrad2/analysis/extracters/window_extracter.py
ipyrad2/analysis/methods/__init__.py
ipyrad2/analysis/methods/admixture.py
ipyrad2/analysis/methods/bpp.py
ipyrad2/analysis/methods/bpp_posteriors.py
ipyrad2/analysis/methods/bpp_summary.py
ipyrad2/analysis/methods/common.py
ipyrad2/analysis/methods/dapc.py
ipyrad2/analysis/methods/pca.py
ipyrad2/analysis/methods/pca_drawing.py
ipyrad2/analysis/methods/snmf.py
ipyrad2/analysis/methods/snps_imputer.py
ipyrad2/analysis/methods/treeslider.py
ipyrad2/analysis/methods/baba/__init__.py
ipyrad2/analysis/methods/baba/models.py
ipyrad2/analysis/methods/baba/runner.py
ipyrad2/analysis/methods/popgen/__init__.py
ipyrad2/analysis/methods/popgen/common.py
ipyrad2/analysis/methods/popgen/estimators.py
ipyrad2/analysis/methods/popgen/models.py
ipyrad2/analysis/methods/popgen/runner.py
ipyrad2/analysis/methods/popgen/seq_backend.py
ipyrad2/analysis/methods/popgen/snp_backend.py
ipyrad2/assembler/__init__.py
ipyrad2/assembler/assemble.py
ipyrad2/assembler/beds.py
ipyrad2/assembler/hdf5_utils.py
ipyrad2/assembler/loci.py
ipyrad2/assembler/paralogs.py
ipyrad2/assembler/read_filters.py
ipyrad2/assembler/sort_utils.py
ipyrad2/assembler/variants.py
ipyrad2/assembler/write_seqs.py
ipyrad2/assembler/write_snps.py
ipyrad2/classic/__init__.py
ipyrad2/classic/cli_classic.py
ipyrad2/cli/__init__.py
ipyrad2/cli/cli_admixture.py
ipyrad2/cli/cli_analysis.py
ipyrad2/cli/cli_assemble.py
ipyrad2/cli/cli_baba.py
ipyrad2/cli/cli_bpp.py
ipyrad2/cli/cli_dapc.py
ipyrad2/cli/cli_demux.py
ipyrad2/cli/cli_denovo.py
ipyrad2/cli/cli_lex.py
ipyrad2/cli/cli_main.py
ipyrad2/cli/cli_map.py
ipyrad2/cli/cli_pca.py
ipyrad2/cli/cli_popgen.py
ipyrad2/cli/cli_snmf.py
ipyrad2/cli/cli_snpex.py
ipyrad2/cli/cli_treeslider.py
ipyrad2/cli/cli_trim.py
ipyrad2/cli/cli_vcf_to_hdf5.py
ipyrad2/cli/cli_wex.py
ipyrad2/cli/command_log.py
ipyrad2/cli/common.py
ipyrad2/demuxer/__init__.py
ipyrad2/demuxer/demux.py
ipyrad2/demuxer/demux_pipeline.py
ipyrad2/demuxer/demux_report.py
ipyrad2/demuxer/match.py
ipyrad2/demuxer/sample_names.py
ipyrad2/denovo/__init__.py
ipyrad2/denovo/align.py
ipyrad2/denovo/cluster.py
ipyrad2/denovo/common.py
ipyrad2/denovo/denovo.py
ipyrad2/denovo/graph.py
ipyrad2/denovo/graph_split.py
ipyrad2/mapper/__init__.py
ipyrad2/mapper/legacy_map_bams.py
ipyrad2/mapper/map_samples_prep.py
ipyrad2/mapper/map_stats.py
ipyrad2/mapper/mapper.py
ipyrad2/trimmer/__init__.py
ipyrad2/trimmer/adapters.fa
ipyrad2/trimmer/trim_fastqs.py
ipyrad2/utils/__init__.py
ipyrad2/utils/exceptions.py
ipyrad2/utils/jit_funcs.py
ipyrad2/utils/kmers.py
ipyrad2/utils/logger.py
ipyrad2/utils/names.py
ipyrad2/utils/params.py
ipyrad2/utils/pops.py
ipyrad2/utils/profiling.py
ipyrad2/utils/progress.py
ipyrad2/utils/seqs.py
ipyrad2/utils/parallel/__init__.py
ipyrad2/utils/parallel/pipeline.py
ipyrad2/utils/parallel/pool.py
scripts/benchmark_denovo_split.py
scripts/migrate_legacy_map_bams.py
tests/ipsimdata.tar.gz
tests/test_analysis_admixture.py
tests/test_analysis_baba.py
tests/test_analysis_bpp.py
tests/test_analysis_cluster_tools.py
tests/test_analysis_extractors.py
tests/test_analysis_pca.py
tests/test_analysis_popgen.py
tests/test_analysis_snmf.py
tests/test_analysis_snp_imputer.py
tests/test_analysis_snp_tools.py
tests/test_analysis_treeslider.py
tests/test_assemble_callable_regions.py
tests/test_assemble_paralogs.py
tests/test_assemble_read_filters.py
tests/test_cli_analysis_help.py
tests/test_cli_assemble_help.py
tests/test_cli_command_log.py
tests/test_cli_demux_help.py
tests/test_cli_denovo_help.py
tests/test_cli_lazy_imports.py
tests/test_cli_map_help.py
tests/test_cli_trim_help.py
tests/test_demux_interrupt.py
tests/test_demux_matching.py
tests/test_denovo.py
tests/test_kmers.py
tests/test_legacy_map_bams.py
tests/test_map_samples_prep.py
tests/test_map_stats.py
tests/test_mapper.py
tests/test_names.py
tests/test_parallel_ctrl_c.py
tests/test_parallel_pipeline.py
tests/test_parallel_pool.py
tests/test_parallel_streaming.py
tests/test_pops.py
tests/test_profiling.py
tests/test_progress_logging.py
tests/test_trim_fastqs.py
tests/test_trim_fastqs_outputs.py
tests/test_version.py