.coveragerc
CHANGES.md
LICENSE
MANIFEST.in
README.rst
paleomix_environment.yaml
setup.cfg
setup.py
tox.ini
docs/Makefile
docs/acknowledgements.rst
docs/conf.py
docs/examples.rst
docs/index.rst
docs/installation.rst
docs/introduction.rst
docs/other_tools.rst
docs/references.rst
docs/related.rst
docs/release.rst
docs/yaml.rst
docs/_static/zonkey/incl_ts_0_tree_rooted.png
docs/_static/zonkey/incl_ts_0_tree_unrooted.png
docs/_static/zonkey/mito_phylo.png
docs/bam_pipeline/configuration.rst
docs/bam_pipeline/filestructure.rst
docs/bam_pipeline/index.rst
docs/bam_pipeline/makefile.rst
docs/bam_pipeline/makefile.yaml
docs/bam_pipeline/overview.rst
docs/bam_pipeline/requirements.rst
docs/bam_pipeline/usage.rst
docs/phylo_pipeline/configuration.rst
docs/phylo_pipeline/filestructure.rst
docs/phylo_pipeline/index.rst
docs/phylo_pipeline/makefile.rst
docs/phylo_pipeline/overview.rst
docs/phylo_pipeline/requirements.rst
docs/phylo_pipeline/usage.rst
docs/troubleshooting/bam_pipeline.rst
docs/troubleshooting/common.rst
docs/troubleshooting/index.rst
docs/troubleshooting/install.rst
docs/troubleshooting/phylo_pipeline.rst
docs/troubleshooting/zonkey_pipeline.rst
docs/zonkey_pipeline/configuration.rst
docs/zonkey_pipeline/filestructure.rst
docs/zonkey_pipeline/index.rst
docs/zonkey_pipeline/overview.rst
docs/zonkey_pipeline/panel.rst
docs/zonkey_pipeline/requirements.rst
docs/zonkey_pipeline/usage.rst
misc/setup_bam_pipeline_example.makefile.yaml
misc/setup_bam_pipeline_example.sh
misc/setup_phylo_pipeline_example.sh
misc/skeleton.py
misc/synthesize_reads.py
paleomix/__init__.py
paleomix/main.py
paleomix/node.py
paleomix/nodegraph.py
paleomix/pipeline.py
paleomix/yaml.py
paleomix.egg-info/PKG-INFO
paleomix.egg-info/SOURCES.txt
paleomix.egg-info/dependency_links.txt
paleomix.egg-info/entry_points.txt
paleomix.egg-info/not-zip-safe
paleomix.egg-info/requires.txt
paleomix.egg-info/top_level.txt
paleomix/atomiccmd/__init__.py
paleomix/atomiccmd/builder.py
paleomix/atomiccmd/command.py
paleomix/atomiccmd/pprint.py
paleomix/atomiccmd/sets.py
paleomix/common/__init__.py
paleomix/common/argparse.py
paleomix/common/bamfiles.py
paleomix/common/bedtools.py
paleomix/common/fileutils.py
paleomix/common/logging.py
paleomix/common/makefile.py
paleomix/common/procs.py
paleomix/common/rtools.py
paleomix/common/sampling.py
paleomix/common/sequences.py
paleomix/common/system.py
paleomix/common/testing.py
paleomix/common/text.py
paleomix/common/timer.py
paleomix/common/utilities.py
paleomix/common/vcffilter.py
paleomix/common/vcfwrap.py
paleomix/common/versions.py
paleomix/common/formats/__init__.py
paleomix/common/formats/_common.py
paleomix/common/formats/_graph.py
paleomix/common/formats/fasta.py
paleomix/common/formats/fastq.py
paleomix/common/formats/msa.py
paleomix/common/formats/newick.py
paleomix/common/formats/phylip.py
paleomix/nodes/__init__.py
paleomix/nodes/adapterremoval.py
paleomix/nodes/bedtools.py
paleomix/nodes/bowtie2.py
paleomix/nodes/bwa.py
paleomix/nodes/commands.py
paleomix/nodes/examl.py
paleomix/nodes/formats.py
paleomix/nodes/mafft.py
paleomix/nodes/mapdamage.py
paleomix/nodes/newick.py
paleomix/nodes/phylip.py
paleomix/nodes/picard.py
paleomix/nodes/raxml.py
paleomix/nodes/samtools.py
paleomix/nodes/sequences.py
paleomix/nodes/validation.py
paleomix/pipelines/__init__.py
paleomix/pipelines/bam/__init__.py
paleomix/pipelines/bam/config.py
paleomix/pipelines/bam/makefile.py
paleomix/pipelines/bam/mkfile.py
paleomix/pipelines/bam/nodes.py
paleomix/pipelines/bam/paths.py
paleomix/pipelines/bam/pipeline.py
paleomix/pipelines/bam/trim_pipeline.py
paleomix/pipelines/bam/parts/__init__.py
paleomix/pipelines/bam/parts/lane.py
paleomix/pipelines/bam/parts/library.py
paleomix/pipelines/bam/parts/prefix.py
paleomix/pipelines/bam/parts/reads.py
paleomix/pipelines/bam/parts/sample.py
paleomix/pipelines/bam/parts/statistics.py
paleomix/pipelines/bam/parts/summary.py
paleomix/pipelines/bam/parts/target.py
paleomix/pipelines/phylo/__init__.py
paleomix/pipelines/phylo/config.py
paleomix/pipelines/phylo/example.py
paleomix/pipelines/phylo/makefile.py
paleomix/pipelines/phylo/mkfile.py
paleomix/pipelines/phylo/pipeline.py
paleomix/pipelines/phylo/parts/__init__.py
paleomix/pipelines/phylo/parts/genotype.py
paleomix/pipelines/phylo/parts/msa.py
paleomix/pipelines/phylo/parts/phylo.py
paleomix/pipelines/zonkey/__init__.py
paleomix/pipelines/zonkey/build_db.py
paleomix/pipelines/zonkey/build_mito.py
paleomix/pipelines/zonkey/build_tped.py
paleomix/pipelines/zonkey/common.py
paleomix/pipelines/zonkey/config.py
paleomix/pipelines/zonkey/database.py
paleomix/pipelines/zonkey/pipeline.py
paleomix/pipelines/zonkey/parts/__init__.py
paleomix/pipelines/zonkey/parts/admixture.py
paleomix/pipelines/zonkey/parts/common.py
paleomix/pipelines/zonkey/parts/mitochondria.py
paleomix/pipelines/zonkey/parts/nuclear.py
paleomix/pipelines/zonkey/parts/report.py
paleomix/pipelines/zonkey/parts/summary.py
paleomix/resources/__init__.py
paleomix/resources/examples/bam_pipeline/makefile.yaml
paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_01.fastq.gz
paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_02.fastq.gz
paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_03.fastq.gz
paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_04.fastq.gz
paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_01.fastq.gz
paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_02.fastq.gz
paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_03.fastq.gz
paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_04.fastq.gz
paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_01.fastq.gz
paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_02.fastq.gz
paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_03.fastq.gz
paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_01.fastq.gz
paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_02.fastq.gz
paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_03.fastq.gz
paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_01.fastq.gz
paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_02.fastq.gz
paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_03.fastq.gz
paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_01.fastq.gz
paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_02.fastq.gz
paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_03.fastq.gz
paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.collapsed.gz
paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.collapsed.truncated.gz
paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.singleton.truncated.gz
paleomix/resources/examples/bam_pipeline/prefixes/rCRS.fasta
paleomix/resources/examples/phylo_pipeline/setup.sh
paleomix/resources/examples/phylo_pipeline/synthesize_reads.py
paleomix/resources/examples/phylo_pipeline/alignment/makefile.yaml
paleomix/resources/examples/phylo_pipeline/alignment/setup.sh
paleomix/resources/examples/phylo_pipeline/alignment/prefixes/bonobo.fasta
paleomix/resources/examples/phylo_pipeline/alignment/prefixes/chimpanzee.fasta
paleomix/resources/examples/phylo_pipeline/alignment/prefixes/gorilla.fasta
paleomix/resources/examples/phylo_pipeline/alignment/prefixes/rCRS.fasta
paleomix/resources/examples/phylo_pipeline/alignment/prefixes/rCRS.fasta.fai
paleomix/resources/examples/phylo_pipeline/alignment/prefixes/sumatran_orangutan.fasta
paleomix/resources/examples/phylo_pipeline/alignment/prefixes/white_handed_gibbon.fasta
paleomix/resources/examples/phylo_pipeline/phylogeny/makefile.yaml
paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.non_coding.bed
paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.protein_coding.CDS.bed
paleomix/resources/reports/zonkey/report.css
paleomix/resources/rscripts/common/requires.r
paleomix/resources/rscripts/zonkey/admixture.r
paleomix/resources/rscripts/zonkey/coverage.r
paleomix/resources/rscripts/zonkey/pca.r
paleomix/resources/rscripts/zonkey/tinytree.r
paleomix/resources/rscripts/zonkey/treemix.r
paleomix/tools/__init__.py
paleomix/tools/cleanup.py
paleomix/tools/coverage.py
paleomix/tools/depths.py
paleomix/tools/dupcheck.py
paleomix/tools/factory.py
paleomix/tools/gtf_to_bed.py
paleomix/tools/rmdup_collapsed.py
paleomix/tools/validate_fastq.py
paleomix/tools/vcf_filter.py
paleomix/tools/vcf_to_fasta.py
paleomix/tools/bam_stats/__init__.py
paleomix/tools/bam_stats/common.py
paleomix/tools/bam_stats/coverage.py
tests/README.rst
tests/node_test.py
tests/nodegraph_test.py
tests/atomiccmd_test/__init__.py
tests/atomiccmd_test/builder_test.py
tests/atomiccmd_test/command_test.py
tests/atomiccmd_test/pprint_test.py
tests/atomiccmd_test/sets_test.py
tests/common_tests/__init__.py
tests/common_tests/bedtools_test.py
tests/common_tests/fileutils_test.py
tests/common_tests/makefile_test.py
tests/common_tests/sampling_test.py
tests/common_tests/sequences_test.py
tests/common_tests/text_test.py
tests/common_tests/utilities_test.py
tests/common_tests/versions_test.py
tests/common_tests/formats_tests/__init__.py
tests/common_tests/formats_tests/fasta_test.py
tests/common_tests/formats_tests/fastq_test.py
tests/common_tests/formats_tests/msa_test.py
tests/common_tests/formats_tests/newick_test.py
tests/common_tests/formats_tests/phylip_test.py
tests/data/empty_file_1
tests/data/empty_file_2
tests/data/rCRS.fasta
tests/data/rCRS.fasta.fai
tests/tools_test/factory_test.py