.gitignore
.travis.yml
CHANGELOG.rst
LICENSE.txt
MANIFEST.in
README.rst
pytest.ini
setup.py
test.bash
dms_tools2/__init__.py
dms_tools2/_cutils.c
dms_tools2/_metadata.py
dms_tools2/barcodes.py
dms_tools2/compareprefs.py
dms_tools2/diffsel.py
dms_tools2/dssp.py
dms_tools2/fracsurvive.py
dms_tools2/ipython_utils.py
dms_tools2/minimap2.py
dms_tools2/pacbio.py
dms_tools2/parseargs.py
dms_tools2/plot.py
dms_tools2/prefs.py
dms_tools2/protstruct.py
dms_tools2/rplot.py
dms_tools2/rplot_Rcode.R
dms_tools2/seqnumbering.py
dms_tools2/sra.py
dms_tools2/syn_selection.py
dms_tools2/utils.py
dms_tools2.egg-info/PKG-INFO
dms_tools2.egg-info/SOURCES.txt
dms_tools2.egg-info/dependency_links.txt
dms_tools2.egg-info/requires.txt
dms_tools2.egg-info/top_level.txt
docs/.gitignore
docs/.nojekyll
docs/Makefile
docs/README.rst
docs/api.rst
docs/bcsubamp.rst
docs/citations.rst
docs/conf.py
docs/diffsel.rst
docs/dms2_batch_bcsubamp.rst
docs/dms2_batch_diffsel.rst
docs/dms2_batch_fracsurvive.rst
docs/dms2_batch_prefs.rst
docs/dms2_bcsubamp.rst
docs/dms2_diffsel.rst
docs/dms2_fracsurvive.rst
docs/dms2_logoplot.rst
docs/dms2_prefs.rst
docs/examples.rst
docs/fracsurvive.rst
docs/index.rst
docs/installation.rst
docs/prefs.rst
docs/programs.rst
docs/weblinks.txt
docs/_static/BarcodedSubampliconDingens2017.jpg
docs/_static/BarcodedSubampliconDoud2016.jpg
docs/_static/BarcodedSubampliconNotes_Jesse.pdf
docs/_static/BarcodedSubampliconNotes_Mike.pdf
docs/_static/BloomLogo.jpg
docs/_static/DiffSelSnippet.jpg
docs/_static/DiffSelWorkflow.jpg
docs/_static/PrefsSnippet.jpg
docs/_static/PrefsWorkflow.jpg
docs/_static/_facetedGGSeqLogo_test_plot.png
docs/_static/_findSigSel.png
docs/_static/_fit_fourParamLogistics_neutplot.png
docs/_static/_fourParamLogistic_neutplot.png
docs/_static/_plotRarefactionCurves.png
docs/_static/_siteSubsetGGSeqLogo_test_plot.png
docs/_static/custom.ccs
docs/_static/frac_survive_example_plot.pdf
docs/_static/frac_survive_example_plot.png
docs/_static/fracsurvive_example.ipynb
docs/_static/fracsurvive_fig.jpg
examples/.gitignore
examples/README.rst
examples/Dingens2017/README.rst
examples/Dingens2017/analysis_notebook.ipynb
examples/Dingens2017/data/BF520c2-Env.fasta
examples/Dingens2017/data/BF520c2_to_HXB2.csv
examples/Dingens2017/data/JRCSFalaninescandata_logbase2_115foldlimit.csv
examples/Dingens2017/data/LAIalaninescandata_logbase2.csv
examples/Dingens2018/.gitignore
examples/Dingens2018/README.md
examples/Dingens2018/analysis_notebook.ipynb
examples/Dingens2018/data/BG505.W6.C2.T332N_env.fasta
examples/Dingens2018/data/BG505_FP_Abs_qPCR_master.csv
examples/Dingens2018/data/BG505_to_HXB2_numbering.txt
examples/Dingens2018/data/BG505pseudovirus_VRC34.01_site_log2IC50foldchange.csv
examples/Dingens2018/data/sitemask_BG505.txt
examples/Doud2016/.gitignore
examples/Doud2016/README.rst
examples/Doud2016/analysis_notebook.ipynb
examples/Doud2016/data/1RVX_trimer_sequentialnumbering.dssp
examples/Doud2016/data/1RVX_trimer_sequentialnumbering.pdb
examples/Doud2016/data/HA_alignment.fasta
examples/Doud2016/data/WSN-HA.fasta
examples/Doud2016/data/originalDoud2016prefs/README.rst
examples/Doud2016/data/originalDoud2016prefs/replicate-1_prefs.csv
examples/Doud2016/data/originalDoud2016prefs/replicate-2_prefs.csv
examples/Doud2016/data/originalDoud2016prefs/replicate-3_prefs.csv
examples/Doud2016/results/codoncounts/mutDNA-1_codoncounts.csv
examples/Doud2016/results/codoncounts/mutDNA-2_codoncounts.csv
examples/Doud2016/results/codoncounts/mutDNA-3_codoncounts.csv
examples/Doud2016/results/codoncounts/mutvirus-1_codoncounts.csv
examples/Doud2016/results/codoncounts/mutvirus-2_codoncounts.csv
examples/Doud2016/results/codoncounts/mutvirus-3_codoncounts.csv
examples/Doud2016/results/codoncounts/wtDNA_codoncounts.csv
examples/Doud2016/results/codoncounts/wtvirus_codoncounts.csv
examples/Doud2016/results/prefs/replicate-1_prefs.csv
examples/Doud2016/results/prefs/replicate-2_prefs.csv
examples/Doud2016/results/prefs/replicate-3_prefs.csv
examples/Doud2016/results/prefs/summary_avgprefs.csv
examples/Doud2017/README.rst
examples/Doud2017/analysis_notebook.ipynb
examples/Doud2017/data/WSN-HA.fasta
examples/Doud2017/data/known_escape.csv
examples/Doud2018/README.md
examples/Doud2018/analysis_notebook.ipynb
examples/Doud2018/data/H1toH3_renumber.csv
examples/Doud2018/data/Overall-WSNHA_merged_prefs_rescaled_H3numbering.csv
examples/Doud2018/data/WSN_HA_reference.fa
examples/Doud2018/data/samples.csv
examples/Haddox2018/README.md
examples/Haddox2018/analysis_notebook.ipynb
examples/Haddox2018/data/5FYL_Env_trimer_rmTER.pdb
examples/Haddox2018/data/5FYL_dssp.txt
examples/Haddox2018/data/5VN3_Env_trimer.pdb
examples/Haddox2018/data/5VN3_dssp.txt
examples/Haddox2018/data/BF520_env.fasta
examples/Haddox2018/data/BG505_env.fasta
examples/Haddox2018/data/Doud2016_HA_replicate-1_prefs.csv
examples/Haddox2018/data/Doud2016_HA_replicate-2_prefs.csv
examples/Haddox2018/data/Doud2016_HA_replicate-3_prefs.csv
examples/Haddox2018/data/Env_protalignment_manualtweaks.fasta
examples/Haddox2018/data/Env_regions.csv
examples/Haddox2018/data/HIV1_FLT_2016_env_DNA.fasta
examples/Haddox2018/data/LAI_env.fasta
examples/Lee2018/README.md
examples/Lee2018/analysis_notebook.ipynb
examples/Lee2018/max_frequency_analysis.ipynb
examples/Lee2018/data/.gitignore
examples/Lee2018/data/1RVX_trimer_sequentialnumbering.dssp
examples/Lee2018/data/4O5N_trimer.dssp
examples/Lee2018/data/BG505_to_BF520_prefs_dist.csv
examples/Lee2018/data/Env_BF520_replicate-1_prefs_rescaled.csv
examples/Lee2018/data/Env_BF520_replicate-2_prefs_rescaled.csv
examples/Lee2018/data/Env_BF520_replicate-3_prefs_rescaled.csv
examples/Lee2018/data/H1toH3_renumber.csv
examples/Lee2018/data/H3_human_alignment.fa
examples/Lee2018/data/H3_swine_alignment.fa
examples/Lee2018/data/H3renumbering_scheme.csv
examples/Lee2018/data/Perth09_HA_reference.fa
examples/Lee2018/data/Perth2009_WSN_aa_align.fa
examples/Lee2018/data/Perth2009_compareprefs_renumber.csv
examples/Lee2018/data/WSN_HA_reference.fa
examples/Lee2018/data/WSN_avgprefs_rescaled_H3numbering.csv
examples/Lee2018/data/WSN_avgprefs_rescaled_seqnumbering.csv
examples/Lee2018/data/WSN_compareprefs_renumber.csv
examples/Lee2018/data/WSN_replicate-1_prefs.csv
examples/Lee2018/data/WSN_replicate-2_prefs.csv
examples/Lee2018/data/WSN_replicate-3_prefs.csv
examples/Lee2018/data/abs_conserved_sites.txt
examples/Lee2018/data/clade_specific_sites.txt
examples/Lee2018/data/domains.csv
examples/Lee2018/data/flu_h3n2_ha_1968_2018_30v_unpassaged_frequencies.json.gz
examples/Lee2018/data/flu_h3n2_ha_1968_2018_30v_unpassaged_tree.json.gz
examples/Lee2018/data/flu_h3n2_ha_1968_2018_6v_frequencies.json.gz
examples/Lee2018/data/flu_h3n2_ha_1968_2018_6v_tree.json.gz
examples/Lee2018/data/wolf_epitope_sites.csv
scripts/dms2_batch_bcsubamp
scripts/dms2_batch_diffsel
scripts/dms2_batch_fracsurvive
scripts/dms2_batch_prefs
scripts/dms2_bcsubamp
scripts/dms2_diffsel
scripts/dms2_fracsurvive
scripts/dms2_logoplot
scripts/dms2_prefs
tests/.gitignore
tests/README.rst
tests/profile_pacbio.py
tests/test_batch_bcsubamp.py
tests/test_batch_diffsel.py
tests/test_batch_fracsurvive.py
tests/test_batch_prefs.py
tests/test_bcsubamp.py
tests/test_build_barcode_variant_table.py
tests/test_convertCountsFormat.py
tests/test_diffsel.py
tests/test_dssp.py
tests/test_fastqfromsra.py
tests/test_fracsurvive.py
tests/test_inferprefsbyratio.py
tests/test_logoplot_diffsel.py
tests/test_logoplot_fracsurvive.py
tests/test_logoplot_muteffects.py
tests/test_logoplot_prefs.py
tests/test_minimap2_multi_alignments.py
tests/test_pacbio_ccs.py
tests/test_pacbio_ccs_align.py
tests/test_pystan_compile.py
tests/test_renumbersites.py
tests/test_site_inferprefs.py
tests/barcodeInfoToCodonVariantTable_input_files/library-1_test_codoncounts.csv
tests/barcodeInfoToCodonVariantTable_input_files/previous_codoncounts.csv
tests/barcodeInfoToCodonVariantTable_input_files/test_bcinfo.txt.gz
tests/bcsubamp_input_files/WSN-HA.fasta
tests/bcsubamp_input_files/expected_codonmuttypes.csv
tests/bcsubamp_input_files/sample-1_R1.fastq.gz
tests/bcsubamp_input_files/sample-1_R2.fastq.gz
tests/bcsubamp_input_files/sample-2_R1.fastq.gz
tests/bcsubamp_input_files/sample-2_R2.fastq.gz
tests/build_barcode_variant_table_files/barcode_lookup.csv
tests/build_barcode_variant_table_files/mut_acc_df.csv
tests/build_barcode_variant_table_files/processed_CCSs.csv
tests/convertCountsFormat_input_files/dms_tools2_format.csv
tests/convertCountsFormat_input_files/dms_tools_format.txt
tests/count_codonvariant_files/PacBio_amplicon.gb
tests/count_codonvariant_files/barcode_variant_table.csv
tests/count_codonvariant_files/fates.csv
tests/count_codonvariant_files/library-1_plasmid_R1.fastq
tests/count_codonvariant_files/library-1_plasmid_R2.fastq
tests/count_codonvariant_files/library-1_uninduced_R1.fastq
tests/count_codonvariant_files/library-1_uninduced_R2.fastq
tests/count_codonvariant_files/library-2_plasmid_R1.fastq
tests/count_codonvariant_files/library-2_plasmid_R2.fastq
tests/count_codonvariant_files/n_variants.csv
tests/count_codonvariant_files/variant_counts.csv
tests/diffsel_input_files/.gitignore
tests/diffsel_input_files/L1_H17L19_c1_r1counts.csv
tests/diffsel_input_files/L1_H17L19_c3_r1counts.csv
tests/diffsel_input_files/L1_mock_r1counts.csv
tests/diffsel_input_files/err_counts.csv
tests/diffsel_input_files/no_err_counts.csv
tests/diffsel_input_files/expected_output/c1-mincounts0_mutdiffsel.csv
tests/diffsel_input_files/expected_output/c1-mincounts0_sitediffsel.csv
tests/diffsel_input_files/expected_output/c1-mincounts10_mutdiffsel.csv
tests/diffsel_input_files/expected_output/c1-mincounts10_sitediffsel.csv
tests/diffsel_input_files/expected_output/c3-mincounts0_mutdiffsel.csv
tests/diffsel_input_files/expected_output/c3-mincounts0_sitediffsel.csv
tests/diffsel_input_files/expected_output/c3-mincounts10_mutdiffsel.csv
tests/diffsel_input_files/expected_output/c3-mincounts10_sitediffsel.csv
tests/diffsel_input_files/expected_output/errors-c1-mincounts0_mutdiffsel.csv
tests/diffsel_input_files/expected_output/errors-c1-mincounts0_sitediffsel.csv
tests/diffsel_input_files/expected_output/errors-c3-mincounts0_mutdiffsel.csv
tests/diffsel_input_files/expected_output/errors-c3-mincounts0_sitediffsel.csv
tests/dssp_input_files/1RVX_trimer_sequentialnumbering.dssp
tests/dssp_input_files/expected_output.csv
tests/fracsurvive_input_files/H17L19-c1-1_codoncounts.csv
tests/fracsurvive_input_files/H17L19-c1-2_codoncounts.csv
tests/fracsurvive_input_files/H17L19-c1-3_codoncounts.csv
tests/fracsurvive_input_files/H17L19-c3-1_codoncounts.csv
tests/fracsurvive_input_files/H17L19-c3-2_codoncounts.csv
tests/fracsurvive_input_files/H17L19-c3-3_codoncounts.csv
tests/fracsurvive_input_files/H18S415-1_codoncounts.csv
tests/fracsurvive_input_files/H18S415-2_codoncounts.csv
tests/fracsurvive_input_files/H18S415-3_codoncounts.csv
tests/fracsurvive_input_files/err-ctrl_codoncounts.csv
tests/fracsurvive_input_files/mock-1_codoncounts.csv
tests/fracsurvive_input_files/mock-2_codoncounts.csv
tests/fracsurvive_input_files/mock-3_codoncounts.csv
tests/fracsurvive_input_files/expected_output/mincounts0_mutfracsurvive.csv
tests/fracsurvive_input_files/expected_output/mincounts0_sitefracsurvive.csv
tests/fracsurvive_input_files/expected_output/mincounts10_mutfracsurvive.csv
tests/fracsurvive_input_files/expected_output/mincounts10_sitefracsurvive.csv
tests/fracsurvive_input_files/expected_output/summary_H17L19-c1-meanmutfracsurvive.csv
tests/fracsurvive_input_files/expected_output/summary_H17L19-c1-meansitefracsurvive.csv
tests/fracsurvive_input_files/expected_output/summary_H17L19-c1-medianmutfracsurvive.csv
tests/fracsurvive_input_files/expected_output/summary_H17L19-c1-mediansitefracsurvive.csv
tests/fracsurvive_input_files/expected_output/summary_H17L19-c3-meanmutfracsurvive.csv
tests/fracsurvive_input_files/expected_output/summary_H17L19-c3-meansitefracsurvive.csv
tests/fracsurvive_input_files/expected_output/summary_H17L19-c3-medianmutfracsurvive.csv
tests/fracsurvive_input_files/expected_output/summary_H17L19-c3-mediansitefracsurvive.csv
tests/func_score_to_gpm_input_files/func_score_to_gpm_test.csv
tests/logoplot_input_files/HA_fracsurvive.csv
tests/logoplot_input_files/HA_mutdiffsel.csv
tests/logoplot_input_files/HA_prefs.csv
tests/logoplot_input_files/continuous_overlay.csv
tests/logoplot_input_files/diffsel_overlay.csv
tests/logoplot_input_files/discrete_overlay.csv
tests/logoplot_input_files/wildtypeoverlayfile.csv
tests/pacbio_ccs_files/README.md
tests/pacbio_ccs_files/test_ccs.bam
tests/pacbio_ccs_files/test_report.txt
tests/pacbio_files/CCSs-1.bam
tests/pacbio_files/CCSs-2.bam
tests/pacbio_files/align_stats_aligned.csv
tests/pacbio_files/align_stats_gene.csv
tests/pacbio_files/alignment_info.csv
tests/pacbio_files/flu-wsn.gb
tests/pacbio_files/targets-double-syn.fasta
tests/pacbio_files/targets.fasta
tests/prefs_input_files/bayesian-replicate-1_prefs.csv
tests/prefs_input_files/bayesian-replicate-2_prefs.csv
tests/prefs_input_files/mutDNA-1_codoncounts.csv
tests/prefs_input_files/mutDNA-2_codoncounts.csv
tests/prefs_input_files/mutvirus-1_codoncounts.csv
tests/prefs_input_files/mutvirus-2_codoncounts.csv
tests/prefs_input_files/ratio-replicate-1_prefs.csv
tests/prefs_input_files/ratio-replicate-2_prefs.csv
tests/prefs_input_files/summary-bayesian_avgprefs.csv
tests/prefs_input_files/summary-ratio_avgprefs.csv
tests/prefs_input_files/wtDNA_codoncounts.csv