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setup.py
misc/setup_bam_pipeline_example.makefile.yaml
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misc/setup_phylo_pipeline_example.sh
misc/skeleton.py
misc/synthesize_reads.py
paleomix/__init__.py
paleomix/config.py
paleomix/logger.py
paleomix/main.py
paleomix/node.py
paleomix/nodegraph.py
paleomix/pipeline.py
paleomix/ui.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/bamfiles.py
paleomix/common/bedtools.py
paleomix/common/console.py
paleomix/common/fileutils.py
paleomix/common/makefile.py
paleomix/common/procs.py
paleomix/common/rtools.py
paleomix/common/sampling.py
paleomix/common/sequences.py
paleomix/common/signals.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/gatk.py
paleomix/nodes/mafft.py
paleomix/nodes/mapdamage.py
paleomix/nodes/misc.py
paleomix/nodes/newick.py
paleomix/nodes/phylip.py
paleomix/nodes/picard.py
paleomix/nodes/raxml.py
paleomix/nodes/samtools.py
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paleomix/resources/__init__.py
paleomix/resources/__init__.pyc
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paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R1_01.fastq.gz
paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R1_02.fastq.gz
paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R1_03.fastq.gz
paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R1_04.fastq.gz
paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R2_01.fastq.gz
paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R2_02.fastq.gz
paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R2_03.fastq.gz
paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R2_04.fastq.gz
paleomix/resources/examples/bam_pipeline/000_data/GCTCTG_L1_R1_01.fastq.gz
paleomix/resources/examples/bam_pipeline/000_data/GCTCTG_L1_R1_02.fastq.gz
paleomix/resources/examples/bam_pipeline/000_data/GCTCTG_L1_R1_03.fastq.gz
paleomix/resources/examples/bam_pipeline/000_data/GCTCTG_L2.bam
paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L1_R1_01.fastq.gz
paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L1_R1_02.fastq.gz
paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L1_R1_03.fastq.gz
paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R1_01.fastq.gz
paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R1_02.fastq.gz
paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R1_03.fastq.gz
paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R2_01.fastq.gz
paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R2_02.fastq.gz
paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R2_03.fastq.gz
paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2/reads.collapsed.gz
paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2/reads.collapsed.truncated.gz
paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2/reads.singleton.truncated.gz
paleomix/resources/examples/bam_pipeline/000_prefixes/rCRS.fasta
paleomix/resources/examples/nature_protocols/alignment/000_makefile.yaml
paleomix/resources/examples/nature_protocols/alignment/000_prefixes/README
paleomix/resources/examples/nature_protocols/alignment/000_prefixes/setup.sh
paleomix/resources/examples/nature_protocols/alignment/000_rawreads/setup.sh
paleomix/resources/examples/nature_protocols/alignment/000_rawreads/06_3928A/000_ENA
paleomix/resources/examples/nature_protocols/alignment/000_rawreads/06_3928A/000_README
paleomix/resources/examples/nature_protocols/alignment/000_rawreads/DDR7602/000_ENA
paleomix/resources/examples/nature_protocols/alignment/000_rawreads/DDR7602/000_README
paleomix/resources/examples/nature_protocols/alignment/000_rawreads/LBUS5/000_ENA
paleomix/resources/examples/nature_protocols/alignment/000_rawreads/LBUS5/000_README
paleomix/resources/examples/nature_protocols/alignment/000_rawreads/M-0182896/000_ENA
paleomix/resources/examples/nature_protocols/alignment/000_rawreads/M-0182896/000_README
paleomix/resources/examples/nature_protocols/alignment/000_rawreads/NL07434/000_ENA
paleomix/resources/examples/nature_protocols/alignment/000_rawreads/NL07434/000_README
paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13527/000_ENA
paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13527/000_README
paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13626/000_ENA
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paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P17777/000_ENA
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paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1845A/000_ENA
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paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1889/000_ENA
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paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/5pCtoT_freq.txt
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paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Length_plot.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Runtime_log.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_correct_prob.csv
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paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/lgdistribution.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/misincorporation.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/3pGtoA_freq.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/5pCtoT_freq.txt
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paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Length_plot.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Runtime_log.txt
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paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/misincorporation.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/3pGtoA_freq.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/5pCtoT_freq.txt
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paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Runtime_log.txt
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paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/misincorporation.txt
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paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/5pCtoT_freq.txt
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paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Length_plot.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Runtime_log.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_correct_prob.csv
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paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/misincorporation.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/3pGtoA_freq.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/5pCtoT_freq.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Fragmisincorporation_plot.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Length_plot.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Runtime_log.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_correct_prob.csv
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paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/dnacomp.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/dnacomp_genome.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/lgdistribution.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/misincorporation.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/3pGtoA_freq.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/5pCtoT_freq.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Fragmisincorporation_plot.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Length_plot.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Runtime_log.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_correct_prob.csv
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