CHANGES.md
MANIFEST.in
README.rst
pylint.conf
setup.py
licenses/gpl.txt
licenses/mit.txt
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/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
paleomix/nodes/sequences.py
paleomix/nodes/validation.py
paleomix/resources/__init__.py
paleomix/resources/__init__.pyc
paleomix/resources/examples/bam_pipeline/000_makefile.yaml
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/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/example_results/alignment/M-0182896.Pi_mito.coverage
paleomix/resources/examples/nature_protocols/example_results/alignment/M-0182896.Pi_mito.depths
paleomix/resources/examples/nature_protocols/example_results/alignment/M-0182896.Pi_nucl.coverage
paleomix/resources/examples/nature_protocols/example_results/alignment/M-0182896.Pi_nucl.depths
paleomix/resources/examples/nature_protocols/example_results/alignment/M-0182896.summary
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.coverage
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.depths
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.coverage
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.depths
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.summary
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.coverage
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.depths
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.coverage
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.depths
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.summary
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/3pGtoA_freq.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/5pCtoT_freq.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Fragmisincorporation_plot.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Length_plot.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Runtime_log.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_correct_prob.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_hist.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_iter_summ_stat.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_post_pred.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_trace.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/dnacomp.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/dnacomp_genome.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/lgdistribution.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/misincorporation.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/3pGtoA_freq.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/5pCtoT_freq.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Fragmisincorporation_plot.pdf
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
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_hist.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_iter_summ_stat.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_post_pred.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_trace.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/dnacomp.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/dnacomp_genome.csv
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
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Fragmisincorporation_plot.pdf
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
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_correct_prob.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_hist.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_iter_summ_stat.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_post_pred.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_trace.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/dnacomp.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/dnacomp_genome.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/lgdistribution.txt
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
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Fragmisincorporation_plot.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Length_plot.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Runtime_log.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_correct_prob.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_hist.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_iter_summ_stat.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_post_pred.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_trace.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/dnacomp.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/dnacomp_genome.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/lgdistribution.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/misincorporation.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/3pGtoA_freq.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/5pCtoT_freq.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Fragmisincorporation_plot.pdf
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
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_hist.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_iter_summ_stat.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_post_pred.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_trace.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/dnacomp.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/dnacomp_genome.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/lgdistribution.txt
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
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_hist.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_iter_summ_stat.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_post_pred.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_trace.pdf
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
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_hist.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_iter_summ_stat.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_post_pred.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_trace.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/dnacomp.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/dnacomp_genome.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/lgdistribution.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/misincorporation.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/3pGtoA_freq.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/5pCtoT_freq.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Fragmisincorporation_plot.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Length_plot.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Runtime_log.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_correct_prob.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_hist.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_iter_summ_stat.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_post_pred.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_trace.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/dnacomp.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/dnacomp_genome.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/lgdistribution.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/misincorporation.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/3pGtoA_freq.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/5pCtoT_freq.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Fragmisincorporation_plot.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Length_plot.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Runtime_log.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_correct_prob.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_hist.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_iter_summ_stat.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_post_pred.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_trace.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/dnacomp.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/dnacomp_genome.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/lgdistribution.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/misincorporation.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/3pGtoA_freq.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/5pCtoT_freq.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Fragmisincorporation_plot.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Length_plot.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Runtime_log.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_correct_prob.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_hist.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_iter_summ_stat.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_post_pred.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_trace.pdf
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/dnacomp.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/dnacomp_genome.csv
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/lgdistribution.txt
paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/misincorporation.txt
paleomix/resources/examples/nature_protocols/example_results/profiling/M.0182896.NO.UDG.txt
paleomix/resources/examples/nature_protocols/example_results/profiling/M.0182896.UDG.txt
paleomix/resources/examples/nature_protocols/example_results/profiling/M.0182896.UDGa.txt
paleomix/resources/examples/nature_protocols/example_results/profiling/M.0182896.UDGb.txt
paleomix/resources/examples/nature_protocols/example_results/profiling/M.0182896.UDGc.txt
paleomix/resources/examples/nature_protocols/example_results/profiling/Pi1845A.id.CGCTAT.txt
paleomix/resources/examples/nature_protocols/example_results/profiling/Pi1889.id.CTTGTA.txt
paleomix/resources/examples/nature_protocols/example_results/profiling/Pi1889.id.GGCTAC.txt
paleomix/resources/examples/nature_protocols/example_results/profiling/Pi1889.id.TAGCTT.txt
paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Figure_Krona_M.0182896.all.html
paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Figure_Krona_Pi1845A.all.html
paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Figure_Krona_Pi1889.all.html
paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Krona_M.0182896.all.txt
paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Krona_Pi1845A.all.txt
paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Krona_Pi1845A.pdf
paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Krona_Pi1889.all.txt
paleomix/resources/examples/nature_protocols/example_results/profiling/krona/M.0182896.all.txt
paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Pi1889.all.txt
paleomix/resources/examples/nature_protocols/example_results/profiling/results/Barplot_class.pdf
paleomix/resources/examples/nature_protocols/example_results/profiling/results/Clustering_genus.pdf
paleomix/resources/examples/nature_protocols/example_results/profiling/results/Distances_genus.txt
paleomix/resources/examples/nature_protocols/example_results/profiling/results/Diversity_genus.txt
paleomix/resources/examples/nature_protocols/example_results/profiling/results/Heatmap_genus.pdf
paleomix/resources/examples/nature_protocols/example_results/profiling/results/PCA_genus.pdf
paleomix/resources/examples/nature_protocols/example_results/profiling/results/PCOA_genus.pdf
paleomix/resources/examples/nature_protocols/example_results/profiling/results/Potato_merged.csv
paleomix/resources/examples/nature_protocols/example_results/profiling/results/Potato_merged_profiles.csv
paleomix/resources/examples/nature_protocols/example_results/profiling/results/Relative_abundances_genus.csv
paleomix/resources/examples/nature_protocols/example_results/profiling/results/Taxon_count_genus.txt
paleomix/resources/examples/nature_protocols/phylogeny/000_makefile.yaml
paleomix/resources/examples/nature_protocols/phylogeny/select_highly_covered_genes.py
paleomix/resources/examples/nature_protocols/phylogeny/summarize_heterozygosity.py
paleomix/resources/examples/nature_protocols/profiling/build_all_profiles.sh
paleomix/resources/examples/nature_protocols/profiling/build_profile.sh
paleomix/resources/examples/nature_protocols/profiling/metagenomic_profile.R
paleomix/resources/examples/phylo_pipeline/setup.sh
paleomix/resources/examples/phylo_pipeline/synthesize_reads.py
paleomix/resources/examples/phylo_pipeline/alignment/000_makefile.yaml
paleomix/resources/examples/phylo_pipeline/alignment/setup.sh
paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/bonobo.fasta
paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/chimpanzee.fasta
paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/gorilla.fasta
paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/rCRS.fasta
paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/rCRS.fasta.fai
paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/sumatran_orangutan.fasta
paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/white_handed_gibbon.fasta
paleomix/resources/examples/phylo_pipeline/phylogeny/000_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/cat.py
paleomix/tools/cleanup.py
paleomix/tools/coverage.py
paleomix/tools/depths.py
paleomix/tools/dupcheck.py
paleomix/tools/duphist.py
paleomix/tools/ena.py
paleomix/tools/factory.py
paleomix/tools/genotype.py
paleomix/tools/gtf_to_bed.py
paleomix/tools/retable.py
paleomix/tools/rmdup_collapsed.py
paleomix/tools/sample_pileup.py
paleomix/tools/vcf_filter.py
paleomix/tools/vcf_to_fasta.py
paleomix/tools/bam_pipeline/__init__.py
paleomix/tools/bam_pipeline/config.py
paleomix/tools/bam_pipeline/makefile.py
paleomix/tools/bam_pipeline/mkfile.py
paleomix/tools/bam_pipeline/nodes.py
paleomix/tools/bam_pipeline/paths.py
paleomix/tools/bam_pipeline/pipeline.py
paleomix/tools/bam_pipeline/remap.py
paleomix/tools/bam_pipeline/trim_pipeline.py
paleomix/tools/bam_pipeline/parts/__init__.py
paleomix/tools/bam_pipeline/parts/lane.py
paleomix/tools/bam_pipeline/parts/library.py
paleomix/tools/bam_pipeline/parts/prefix.py
paleomix/tools/bam_pipeline/parts/reads.py
paleomix/tools/bam_pipeline/parts/sample.py
paleomix/tools/bam_pipeline/parts/statistics.py
paleomix/tools/bam_pipeline/parts/summary.py
paleomix/tools/bam_pipeline/parts/target.py
paleomix/tools/bam_stats/__init__.py
paleomix/tools/bam_stats/common.py
paleomix/tools/bam_stats/coverage.py
paleomix/tools/phylo_pipeline/__init__.py
paleomix/tools/phylo_pipeline/config.py
paleomix/tools/phylo_pipeline/makefile.py
paleomix/tools/phylo_pipeline/mkfile.py
paleomix/tools/phylo_pipeline/pipeline.py
paleomix/tools/phylo_pipeline/parts/__init__.py
paleomix/tools/phylo_pipeline/parts/genotype.py
paleomix/tools/phylo_pipeline/parts/msa.py
paleomix/tools/phylo_pipeline/parts/paml.py
paleomix/tools/phylo_pipeline/parts/phylo.py
paleomix/tools/zonkey/__init__.py
paleomix/tools/zonkey/build_db.py
paleomix/tools/zonkey/build_mito.py
paleomix/tools/zonkey/build_tped.py
paleomix/tools/zonkey/common.py
paleomix/tools/zonkey/config.py
paleomix/tools/zonkey/database.py
paleomix/tools/zonkey/pipeline.py
paleomix/tools/zonkey/parts/__init__.py
paleomix/tools/zonkey/parts/admixture.py
paleomix/tools/zonkey/parts/common.py
paleomix/tools/zonkey/parts/mitochondria.py
paleomix/tools/zonkey/parts/nuclear.py
paleomix/tools/zonkey/parts/report.py
paleomix/tools/zonkey/parts/summary.py
paleomix/yaml/CHANGES
paleomix/yaml/LICENSE
paleomix/yaml/PKG-INFO
paleomix/yaml/README
paleomix/yaml/__init__.py
paleomix/yaml/lib2/__init__.py
paleomix/yaml/lib2/composer.py
paleomix/yaml/lib2/constructor.py
paleomix/yaml/lib2/dumper.py
paleomix/yaml/lib2/emitter.py
paleomix/yaml/lib2/error.py
paleomix/yaml/lib2/events.py
paleomix/yaml/lib2/loader.py
paleomix/yaml/lib2/nodes.py
paleomix/yaml/lib2/parser.py
paleomix/yaml/lib2/reader.py
paleomix/yaml/lib2/representer.py
paleomix/yaml/lib2/resolver.py
paleomix/yaml/lib2/scanner.py
paleomix/yaml/lib2/serializer.py
paleomix/yaml/lib2/tokens.py
tests/.coveragerc
tests/README.rst
tests/node_test.py
tests/nodegraph_test.py
tests/setup.sh
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/bwa/README
tests/bwa/run.sh
tests/bwa/testcases/case_01a/README
tests/bwa/testcases/case_01a/prefix.fasta
tests/bwa/testcases/case_01a/reads1.fasta
tests/bwa/testcases/case_01a/reads2.fasta
tests/bwa/testcases/case_01b/README
tests/bwa/testcases/case_01b/prefix.fasta
tests/bwa/testcases/case_01b/reads1.fasta
tests/bwa/testcases/case_01b/reads2.fasta
tests/bwa/testcases/case_02/README
tests/bwa/testcases/case_02/prefix.fasta
tests/bwa/testcases/case_02/reads1.fasta
tests/bwa/testcases/case_02/reads2.fasta
tests/bwa/testcases/case_02/run.sh
tests/bwa/testcases/case_03/README
tests/bwa/testcases/case_03/prefix.fasta
tests/bwa/testcases/case_03/reads.fasta
tests/bwa/testcases/case_03/run.sh
tests/bwa/testcases/case_04/README
tests/bwa/testcases/case_04/prefix.fasta
tests/bwa/testcases/case_04/reads.fasta
tests/bwa/testcases/case_04/results.sam
tests/bwa/testcases/case_04/run.sh
tests/common_tests/__init__.py
tests/common_tests/bedtools_tests.py
tests/common_tests/fileutils_test.py
tests/common_tests/makefile_test.py
tests/common_tests/sampling_tests.py
tests/common_tests/sequences_test.py
tests/common_tests/signals_test.py
tests/common_tests/text_tests.py
tests/common_tests/utilities_test.py
tests/common_tests/versions_tests.py
tests/common_tests/formats_tests/__init__.py
tests/common_tests/formats_tests/fasta_test.py
tests/common_tests/formats_tests/msa_test.py
tests/common_tests/formats_tests/newick_tests.py
tests/common_tests/formats_tests/phylip_test.py
tests/data/empty_file_1
tests/data/empty_file_2
tests/data/empty_file_3
tests/data/fasta_file.fasta
tests/data/fasta_file.fasta.bz2
tests/data/fasta_file.fasta.gz
tests/data/non_empty_file_1
tests/data/non_empty_file_2
tests/data/non_empty_file_3
tests/data/rCRS.fasta
tests/data/rCRS.fasta.fai
tests/data/simple.yaml
tests/data/timestamp_a_older
tests/data/timestamp_a_younger
tests/data/timestamp_b_older
tests/data/timestamp_b_younger
tests/data/alignments/library_1.bam
tests/data/alignments/library_2.bam
tests/data/raw_reads/pe_reads_R1_001.fastq.gz
tests/data/raw_reads/pe_reads_R1_002.fastq.gz
tests/data/raw_reads/pe_reads_R2_001.fastq.gz
tests/data/raw_reads/pe_reads_R2_002.fastq.gz
tests/data/raw_reads/se_reads_R1_001.fastq.gz
tests/data/raw_reads/se_reads_R1_002.fastq.gz
tests/data/sim_reads/mate_1.fastq.gz
tests/data/sim_reads/mate_2.fastq.gz
tests/tools_test/factory_test.py