├── .gitignore ├── .gitmodules ├── 0_create_gtf.ipynb ├── 1_Nano-DMS-MaP_workflow.ipynb ├── 2_plot_isoquant.ipynb ├── 3_plot_mutation_rate_and_coverage_per_isoform.ipynb ├── 4_plot_per_isoform_reactivity.ipynb ├── 5_subsampling.ipynb ├── LICENSE ├── README.md ├── Samplesheet_example.xlsx ├── environment.yml ├── figures ├── coverage_plots │ ├── RT1_unspliced1.svg │ ├── RT2_Env10_RT3_Rev7.svg │ ├── RT2_Env11_RT3_Rev8.svg │ ├── RT2_Env12_RT3_Rev9.svg │ ├── RT2_Env13_RT3_Nef5.svg │ ├── RT2_Env14_RT3_Rev10.svg │ ├── RT2_Env15_RT3_Rev11.svg │ ├── RT2_Env17_RT3_Nef9.svg │ ├── RT2_Env1_RT3_Nef2.svg │ ├── RT2_Env20_RT3_Nef11.svg │ ├── RT2_Env2_RT3_Rev1.svg │ ├── RT2_Env3_RT3_Rev2.svg │ ├── RT2_Env4_RT3_Rev3.svg │ ├── RT2_Env5_RT3_Nef3.svg │ ├── RT2_Env6_RT3_Rev4.svg │ ├── RT2_Env7_RT3_Rev5.svg │ ├── RT2_Env8_RT3_Rev6.svg │ ├── RT2_Env9_RT3_Nef4.svg │ ├── RT2_Tat5_RT3_Tat1.svg │ ├── RT2_Tat6_RT3_Tat2.svg │ ├── RT2_Tat7_RT3_Tat3.svg │ ├── RT2_Tat8_RT3_Tat4.svg │ ├── RT2_Vif2_RT3_Vif1.svg │ ├── RT2_Vpr3_RT3_Vpr1.svg │ ├── RT2_Vpr4_RT3_Vpr2.svg │ ├── RT3_Nef19.svg │ ├── RT3_Rev12.svg │ ├── RT3_sORF1.svg │ ├── RT3_sORF3.svg │ ├── log_RT1_unspliced1.svg │ ├── log_RT2_Env10_RT3_Rev7.svg │ ├── log_RT2_Env11_RT3_Rev8.svg │ ├── log_RT2_Env12_RT3_Rev9.svg │ ├── log_RT2_Env13_RT3_Nef5.svg │ ├── log_RT2_Env14_RT3_Rev10.svg │ ├── log_RT2_Env15_RT3_Rev11.svg │ ├── log_RT2_Env17_RT3_Nef9.svg │ ├── log_RT2_Env1_RT3_Nef2.svg │ ├── log_RT2_Env20_RT3_Nef11.svg │ ├── log_RT2_Env2_RT3_Rev1.svg │ ├── log_RT2_Env3_RT3_Rev2.svg │ ├── log_RT2_Env4_RT3_Rev3.svg │ ├── log_RT2_Env5_RT3_Nef3.svg │ ├── log_RT2_Env6_RT3_Rev4.svg │ ├── log_RT2_Env7_RT3_Rev5.svg │ ├── log_RT2_Env8_RT3_Rev6.svg │ ├── log_RT2_Env9_RT3_Nef4.svg │ ├── log_RT2_Tat5_RT3_Tat1.svg │ ├── log_RT2_Tat6_RT3_Tat2.svg │ ├── log_RT2_Tat7_RT3_Tat3.svg │ ├── log_RT2_Tat8_RT3_Tat4.svg │ ├── log_RT2_Vif2_RT3_Vif1.svg │ ├── log_RT2_Vpr3_RT3_Vpr1.svg │ ├── log_RT2_Vpr4_RT3_Vpr2.svg │ ├── log_RT3_Nef19.svg │ ├── log_RT3_Rev12.svg │ ├── log_RT3_sORF1.svg │ └── log_RT3_sORF3.svg ├── coverage_vs_corr.svg ├── isoform_expression │ ├── isoquant_classification_absolute.svg │ ├── isoquant_classification_percent.svg │ ├── isoquant_isoform_count.svg │ └── isoquant_isoform_percent.svg ├── log_coverage_vs_corr.svg ├── log_subsample_coverage_vs_median_pearson_corr_within_rep.svg ├── mut_rates │ ├── RT-FS_log_mut_type_per_nt_bar.svg │ ├── RT-FS_log_mut_type_per_nt_line.svg │ ├── RT-FS_log_mut_type_wo_indel_per_nt_bar.svg │ ├── RT-FS_mut_type_per_nt_bar.svg │ ├── RT-US_log_mut_type_per_nt_bar.svg │ ├── RT-US_log_mut_type_per_nt_line.svg │ ├── RT-US_log_mut_type_wo_indel_per_nt_bar.svg │ ├── RT-US_mut_type_per_nt_bar.svg │ ├── RT1_log_mut_type_per_nt_bar.svg │ ├── RT1_log_mut_type_wo_indel_per_nt_bar.svg │ ├── RT1_mut_type_per_nt_bar.svg │ ├── RT2_log_mut_type_per_nt_bar.svg │ ├── RT2_log_mut_type_wo_indel_per_nt_bar.svg │ ├── RT2_mut_type_per_nt_bar.svg │ ├── log_line_error_per_RT_w_error_bands_stdev.svg │ ├── log_line_error_per_RT_w_per_isoform_error_bands_stdev.svg │ ├── log_line_error_w_per_isoform_error_bands_stdev.svg │ ├── log_line_w_error_bands_per_RT_stdev.svg │ ├── log_line_w_error_bands_stdev.svg │ ├── log_line_w_error_bands_stdev.svg.e541eca8-fec6-4de9-8e74-07820578ad83 │ ├── nanopore_log_snm_rate_box.svg │ ├── nanopore_log_snm_rate_per_nt_box.svg │ ├── nanopore_mut_rate_box.svg │ ├── nanopore_mut_rate_per_nt_box.svg │ ├── nanopore_mut_type_per_nt_log_box.svg │ ├── nanopore_mut_type_per_nt_log_line.svg │ ├── nanopore_snm_rate_box.svg │ └── nanopore_snm_rate_per_nt_box.svg ├── reactivities │ ├── 57mM_AC_correlation.svg │ ├── 57mM_AC_heatmap.svg │ ├── 85mM_AC_correlation.svg │ └── 85mM_AC_heatmap.svg ├── reactivity_correlations │ ├── 85mM_AC_correlation.svg │ ├── 85mM_AC_heatmap.svg │ ├── correlation_57mM_win10.svg │ ├── correlation_57mM_win100.svg │ ├── correlation_57mM_win20.svg │ ├── correlation_57mM_win200.svg │ ├── correlation_57mM_win50.svg │ ├── correlation_85mM_win10.svg │ ├── correlation_85mM_win100.svg │ ├── correlation_85mM_win20.svg │ ├── correlation_85mM_win200.svg │ └── correlation_85mM_win50.svg ├── subsample_coverage_vs_median_pearson_corr.svg ├── subsample_coverage_vs_median_pearson_corr_example_isoforms.svg ├── subsample_coverage_vs_median_pearson_corr_within_rep.svg ├── subsample_ratio_vs_median_pearson_corr_within_rep.svg ├── subsampling │ ├── log_subsample_size_vs_reactivity_corr.svg │ ├── log_subsample_size_vs_reactivity_corr_RT1_unspliced1.svg │ ├── log_subsample_size_vs_reactivity_corr_RT2_Env10_RT3_Rev7.svg │ ├── log_subsample_size_vs_reactivity_corr_RT2_Env11_RT3_Rev8.svg │ ├── log_subsample_size_vs_reactivity_corr_RT2_Env12_RT3_Rev9.svg │ ├── log_subsample_size_vs_reactivity_corr_RT2_Env13_RT3_Nef5.svg │ ├── log_subsample_size_vs_reactivity_corr_RT2_Env14_RT3_Rev10.svg │ ├── log_subsample_size_vs_reactivity_corr_RT2_Env15_RT3_Rev11.svg │ ├── log_subsample_size_vs_reactivity_corr_RT2_Env17_RT3_Nef9.svg │ ├── log_subsample_size_vs_reactivity_corr_RT2_Env1_RT3_Nef2.svg │ ├── log_subsample_size_vs_reactivity_corr_RT2_Env2_RT3_Rev1.svg │ ├── log_subsample_size_vs_reactivity_corr_RT2_Env3_RT3_Rev2.svg │ ├── log_subsample_size_vs_reactivity_corr_RT2_Env4_RT3_Rev3.svg │ ├── log_subsample_size_vs_reactivity_corr_RT2_Env5_RT3_Nef3.svg │ ├── log_subsample_size_vs_reactivity_corr_RT2_Env6_RT3_Rev4.svg │ ├── log_subsample_size_vs_reactivity_corr_RT2_Env7_RT3_Rev5.svg │ ├── log_subsample_size_vs_reactivity_corr_RT2_Env9_RT3_Nef4.svg │ ├── log_subsample_size_vs_reactivity_corr_RT2_Tat5_RT3_Tat1.svg │ ├── log_subsample_size_vs_reactivity_corr_RT2_Tat6_RT3_Tat2.svg │ ├── log_subsample_size_vs_reactivity_corr_RT2_Tat7_RT3_Tat3.svg │ ├── log_subsample_size_vs_reactivity_corr_RT2_Tat8_RT3_Tat4.svg │ ├── log_subsample_size_vs_reactivity_corr_RT2_Vpr3_RT3_Vpr1.svg │ ├── log_subsample_size_vs_reactivity_corr_RT2_Vpr4_RT3_Vpr2.svg │ ├── log_subsample_size_vs_reactivity_corr_RT3_Rev12.svg │ ├── log_subsample_size_vs_reactivity_corr_RT3_sORF1.svg │ ├── log_subsample_size_vs_reactivity_corr_RT3_sORF3.svg │ ├── log_subsample_size_vs_within_rep_reactivity_corr.svg │ ├── subsample_size_vs_reactivity_corr.svg │ └── subsample_size_vs_within_rep_reactivity_corr.svg ├── virtual_gel_2000nt.svg ├── virtual_gel_3000nt.svg └── virtual_gel_6000nt.svg └── references ├── 18S_rRNA.fa ├── HIV1-NL43.fa ├── HIV1-NL43_all_iso_PCR1_2_3.gtf ├── IVT_RNAs ├── HCV_IRES.fa ├── V_chol_gly_riboswitch.fa ├── bact_RNaseP_typeA.fa ├── hc16.fa └── tetrahymena_ribozyme.fa ├── RT-FL-PCR_unspliced1.fa ├── mask_primers_PCR1_2_3.csv └── transcripts_PCR1_2_3 ├── RT1_unspliced1.fa ├── RT1_unspliced1.fa.fai ├── RT1_unspliced1_LAST.bck ├── RT1_unspliced1_LAST.des ├── RT1_unspliced1_LAST.prj ├── RT1_unspliced1_LAST.sds ├── RT1_unspliced1_LAST.ssp ├── RT1_unspliced1_LAST.suf ├── RT1_unspliced1_LAST.tis ├── RT2_Env10_RT3_Rev7.fa ├── RT2_Env10_RT3_Rev7.fa.fai ├── RT2_Env10_RT3_Rev7_LAST.bck ├── RT2_Env10_RT3_Rev7_LAST.des ├── RT2_Env10_RT3_Rev7_LAST.prj ├── RT2_Env10_RT3_Rev7_LAST.sds ├── RT2_Env10_RT3_Rev7_LAST.ssp ├── RT2_Env10_RT3_Rev7_LAST.suf ├── RT2_Env10_RT3_Rev7_LAST.tis ├── RT2_Env11_RT3_Rev8.fa ├── RT2_Env11_RT3_Rev8.fa.fai ├── RT2_Env11_RT3_Rev8_LAST.bck ├── RT2_Env11_RT3_Rev8_LAST.des ├── RT2_Env11_RT3_Rev8_LAST.prj ├── RT2_Env11_RT3_Rev8_LAST.sds ├── RT2_Env11_RT3_Rev8_LAST.ssp ├── RT2_Env11_RT3_Rev8_LAST.suf ├── RT2_Env11_RT3_Rev8_LAST.tis ├── RT2_Env12_RT3_Rev9.fa ├── RT2_Env12_RT3_Rev9.fa.fai ├── RT2_Env12_RT3_Rev9_LAST.bck ├── RT2_Env12_RT3_Rev9_LAST.des ├── RT2_Env12_RT3_Rev9_LAST.prj ├── RT2_Env12_RT3_Rev9_LAST.sds ├── RT2_Env12_RT3_Rev9_LAST.ssp ├── RT2_Env12_RT3_Rev9_LAST.suf ├── RT2_Env12_RT3_Rev9_LAST.tis ├── RT2_Env13_RT3_Nef5.fa ├── RT2_Env13_RT3_Nef5.fa.fai ├── RT2_Env13_RT3_Nef5_LAST.bck ├── RT2_Env13_RT3_Nef5_LAST.des ├── RT2_Env13_RT3_Nef5_LAST.prj ├── RT2_Env13_RT3_Nef5_LAST.sds ├── RT2_Env13_RT3_Nef5_LAST.ssp ├── RT2_Env13_RT3_Nef5_LAST.suf ├── RT2_Env13_RT3_Nef5_LAST.tis ├── RT2_Env14_RT3_Rev10.fa ├── RT2_Env14_RT3_Rev10.fa.fai ├── RT2_Env14_RT3_Rev10_LAST.bck ├── RT2_Env14_RT3_Rev10_LAST.des ├── RT2_Env14_RT3_Rev10_LAST.prj ├── RT2_Env14_RT3_Rev10_LAST.sds ├── RT2_Env14_RT3_Rev10_LAST.ssp ├── RT2_Env14_RT3_Rev10_LAST.suf ├── RT2_Env14_RT3_Rev10_LAST.tis ├── RT2_Env15_RT3_Rev11.fa ├── RT2_Env15_RT3_Rev11.fa.fai ├── RT2_Env15_RT3_Rev11_LAST.bck ├── RT2_Env15_RT3_Rev11_LAST.des ├── RT2_Env15_RT3_Rev11_LAST.prj ├── RT2_Env15_RT3_Rev11_LAST.sds ├── RT2_Env15_RT3_Rev11_LAST.ssp ├── RT2_Env15_RT3_Rev11_LAST.suf ├── RT2_Env15_RT3_Rev11_LAST.tis ├── RT2_Env17_RT3_Nef9.fa ├── RT2_Env17_RT3_Nef9.fa.fai ├── RT2_Env17_RT3_Nef9_LAST.bck ├── RT2_Env17_RT3_Nef9_LAST.des ├── RT2_Env17_RT3_Nef9_LAST.prj ├── RT2_Env17_RT3_Nef9_LAST.sds ├── RT2_Env17_RT3_Nef9_LAST.ssp ├── RT2_Env17_RT3_Nef9_LAST.suf ├── RT2_Env17_RT3_Nef9_LAST.tis ├── RT2_Env18_RT3_Rev13.fa ├── RT2_Env19_RT3_Nef12.fa ├── RT2_Env1_RT3_Nef2.fa ├── RT2_Env1_RT3_Nef2.fa.fai ├── RT2_Env1_RT3_Nef2_LAST.bck ├── RT2_Env1_RT3_Nef2_LAST.des ├── RT2_Env1_RT3_Nef2_LAST.prj ├── RT2_Env1_RT3_Nef2_LAST.sds ├── RT2_Env1_RT3_Nef2_LAST.ssp ├── RT2_Env1_RT3_Nef2_LAST.suf ├── RT2_Env1_RT3_Nef2_LAST.tis ├── RT2_Env20_RT3_Nef11.fa ├── RT2_Env20_RT3_Nef11.fa.fai ├── RT2_Env20_RT3_Nef11_LAST.bck ├── RT2_Env20_RT3_Nef11_LAST.des ├── RT2_Env20_RT3_Nef11_LAST.prj ├── RT2_Env20_RT3_Nef11_LAST.sds ├── RT2_Env20_RT3_Nef11_LAST.ssp ├── RT2_Env20_RT3_Nef11_LAST.suf ├── RT2_Env20_RT3_Nef11_LAST.tis ├── RT2_Env2_RT3_Rev1.fa ├── RT2_Env2_RT3_Rev1.fa.fai ├── RT2_Env2_RT3_Rev1_LAST.bck ├── RT2_Env2_RT3_Rev1_LAST.des ├── RT2_Env2_RT3_Rev1_LAST.prj ├── RT2_Env2_RT3_Rev1_LAST.sds ├── RT2_Env2_RT3_Rev1_LAST.ssp ├── RT2_Env2_RT3_Rev1_LAST.suf ├── RT2_Env2_RT3_Rev1_LAST.tis ├── RT2_Env3_RT3_Rev2.fa ├── RT2_Env3_RT3_Rev2.fa.fai ├── RT2_Env3_RT3_Rev2_LAST.bck ├── RT2_Env3_RT3_Rev2_LAST.des ├── RT2_Env3_RT3_Rev2_LAST.prj ├── RT2_Env3_RT3_Rev2_LAST.sds ├── RT2_Env3_RT3_Rev2_LAST.ssp ├── RT2_Env3_RT3_Rev2_LAST.suf ├── RT2_Env3_RT3_Rev2_LAST.tis ├── RT2_Env4_RT3_Rev3.fa ├── RT2_Env4_RT3_Rev3.fa.fai ├── RT2_Env4_RT3_Rev3_LAST.bck ├── RT2_Env4_RT3_Rev3_LAST.des ├── RT2_Env4_RT3_Rev3_LAST.prj ├── RT2_Env4_RT3_Rev3_LAST.sds ├── RT2_Env4_RT3_Rev3_LAST.ssp ├── RT2_Env4_RT3_Rev3_LAST.suf ├── RT2_Env4_RT3_Rev3_LAST.tis ├── RT2_Env5_RT3_Nef3.fa ├── RT2_Env5_RT3_Nef3.fa.fai ├── RT2_Env5_RT3_Nef3_LAST.bck ├── RT2_Env5_RT3_Nef3_LAST.des ├── RT2_Env5_RT3_Nef3_LAST.prj ├── RT2_Env5_RT3_Nef3_LAST.sds ├── RT2_Env5_RT3_Nef3_LAST.ssp ├── RT2_Env5_RT3_Nef3_LAST.suf ├── RT2_Env5_RT3_Nef3_LAST.tis ├── RT2_Env6_RT3_Rev4.fa ├── RT2_Env6_RT3_Rev4.fa.fai ├── RT2_Env6_RT3_Rev4_LAST.bck ├── RT2_Env6_RT3_Rev4_LAST.des ├── RT2_Env6_RT3_Rev4_LAST.prj ├── RT2_Env6_RT3_Rev4_LAST.sds ├── RT2_Env6_RT3_Rev4_LAST.ssp ├── RT2_Env6_RT3_Rev4_LAST.suf ├── RT2_Env6_RT3_Rev4_LAST.tis ├── RT2_Env7_RT3_Rev5.fa ├── RT2_Env7_RT3_Rev5.fa.fai ├── RT2_Env7_RT3_Rev5_LAST.bck ├── RT2_Env7_RT3_Rev5_LAST.des ├── RT2_Env7_RT3_Rev5_LAST.prj ├── RT2_Env7_RT3_Rev5_LAST.sds ├── RT2_Env7_RT3_Rev5_LAST.ssp ├── RT2_Env7_RT3_Rev5_LAST.suf ├── RT2_Env7_RT3_Rev5_LAST.tis ├── RT2_Env8_RT3_Rev6.fa ├── RT2_Env8_RT3_Rev6.fa.fai ├── RT2_Env8_RT3_Rev6_LAST.bck ├── RT2_Env8_RT3_Rev6_LAST.des ├── RT2_Env8_RT3_Rev6_LAST.prj ├── RT2_Env8_RT3_Rev6_LAST.sds ├── RT2_Env8_RT3_Rev6_LAST.ssp ├── RT2_Env8_RT3_Rev6_LAST.suf ├── RT2_Env8_RT3_Rev6_LAST.tis ├── RT2_Env9_RT3_Nef4.fa ├── RT2_Env9_RT3_Nef4.fa.fai ├── RT2_Env9_RT3_Nef4_LAST.bck ├── RT2_Env9_RT3_Nef4_LAST.des ├── RT2_Env9_RT3_Nef4_LAST.prj ├── RT2_Env9_RT3_Nef4_LAST.sds ├── RT2_Env9_RT3_Nef4_LAST.ssp ├── RT2_Env9_RT3_Nef4_LAST.suf ├── RT2_Env9_RT3_Nef4_LAST.tis ├── RT2_Tat12_RT3_Tat9.fa ├── RT2_Tat5_RT3_Tat1.fa ├── RT2_Tat5_RT3_Tat1.fa.fai ├── RT2_Tat5_RT3_Tat1_LAST.bck ├── RT2_Tat5_RT3_Tat1_LAST.des ├── RT2_Tat5_RT3_Tat1_LAST.prj ├── RT2_Tat5_RT3_Tat1_LAST.sds ├── RT2_Tat5_RT3_Tat1_LAST.ssp ├── RT2_Tat5_RT3_Tat1_LAST.suf ├── RT2_Tat5_RT3_Tat1_LAST.tis ├── RT2_Tat6_RT3_Tat2.fa ├── RT2_Tat6_RT3_Tat2.fa.fai ├── RT2_Tat6_RT3_Tat2_LAST.bck ├── RT2_Tat6_RT3_Tat2_LAST.des ├── RT2_Tat6_RT3_Tat2_LAST.prj ├── RT2_Tat6_RT3_Tat2_LAST.sds ├── RT2_Tat6_RT3_Tat2_LAST.ssp ├── RT2_Tat6_RT3_Tat2_LAST.suf ├── RT2_Tat6_RT3_Tat2_LAST.tis ├── RT2_Tat7_RT3_Tat3.fa ├── RT2_Tat7_RT3_Tat3.fa.fai ├── RT2_Tat7_RT3_Tat3_LAST.bck ├── RT2_Tat7_RT3_Tat3_LAST.des ├── RT2_Tat7_RT3_Tat3_LAST.prj ├── RT2_Tat7_RT3_Tat3_LAST.sds ├── RT2_Tat7_RT3_Tat3_LAST.ssp ├── RT2_Tat7_RT3_Tat3_LAST.suf ├── RT2_Tat7_RT3_Tat3_LAST.tis ├── RT2_Tat8_RT3_Tat4.fa ├── RT2_Tat8_RT3_Tat4.fa.fai ├── RT2_Tat8_RT3_Tat4_LAST.bck ├── RT2_Tat8_RT3_Tat4_LAST.des ├── RT2_Tat8_RT3_Tat4_LAST.prj ├── RT2_Tat8_RT3_Tat4_LAST.sds ├── RT2_Tat8_RT3_Tat4_LAST.ssp ├── RT2_Tat8_RT3_Tat4_LAST.suf ├── RT2_Tat8_RT3_Tat4_LAST.tis ├── RT2_Vif2_RT3_Vif1.fa ├── RT2_Vif2_RT3_Vif1.fa.fai ├── RT2_Vif2_RT3_Vif1_LAST.bck ├── RT2_Vif2_RT3_Vif1_LAST.des ├── RT2_Vif2_RT3_Vif1_LAST.prj ├── RT2_Vif2_RT3_Vif1_LAST.sds ├── RT2_Vif2_RT3_Vif1_LAST.ssp ├── RT2_Vif2_RT3_Vif1_LAST.suf ├── RT2_Vif2_RT3_Vif1_LAST.tis ├── RT2_Vif3_RT3_Vif6.fa ├── RT2_Vif4_RT3_Vif9.fa ├── RT2_Vif5_RT3_Vif8.fa ├── RT2_Vif7.fa ├── RT2_Vpr3_RT3_Vpr1.fa ├── RT2_Vpr3_RT3_Vpr1.fa.fai ├── RT2_Vpr3_RT3_Vpr1_LAST.bck ├── RT2_Vpr3_RT3_Vpr1_LAST.des ├── RT2_Vpr3_RT3_Vpr1_LAST.prj ├── RT2_Vpr3_RT3_Vpr1_LAST.sds ├── RT2_Vpr3_RT3_Vpr1_LAST.ssp ├── RT2_Vpr3_RT3_Vpr1_LAST.suf ├── RT2_Vpr3_RT3_Vpr1_LAST.tis ├── RT2_Vpr4_RT3_Vpr2.fa ├── RT2_Vpr4_RT3_Vpr2.fa.fai ├── RT2_Vpr4_RT3_Vpr2_LAST.bck ├── RT2_Vpr4_RT3_Vpr2_LAST.des ├── RT2_Vpr4_RT3_Vpr2_LAST.prj ├── RT2_Vpr4_RT3_Vpr2_LAST.sds ├── RT2_Vpr4_RT3_Vpr2_LAST.ssp ├── RT2_Vpr4_RT3_Vpr2_LAST.suf ├── RT2_Vpr4_RT3_Vpr2_LAST.tis ├── RT2_unspliced2.fa ├── RT2_unspliced2.fa.fai ├── RT2_unspliced2_LAST.bck ├── RT2_unspliced2_LAST.des ├── RT2_unspliced2_LAST.prj ├── RT2_unspliced2_LAST.sds ├── RT2_unspliced2_LAST.ssp ├── RT2_unspliced2_LAST.suf ├── RT2_unspliced2_LAST.tis ├── RT3_Nef15.fa ├── RT3_Nef16.fa ├── RT3_Nef19.fa ├── RT3_Nef19.fa.fai ├── RT3_Nef19_LAST.bck ├── RT3_Nef19_LAST.des ├── RT3_Nef19_LAST.prj ├── RT3_Nef19_LAST.sds ├── RT3_Nef19_LAST.ssp ├── RT3_Nef19_LAST.suf ├── RT3_Nef19_LAST.tis ├── RT3_Nef20.fa ├── RT3_Nef22.fa ├── RT3_Nef23.fa ├── RT3_Rev12.fa ├── RT3_Rev12.fa.fai ├── RT3_Rev12_LAST.bck ├── RT3_Rev12_LAST.des ├── RT3_Rev12_LAST.prj ├── RT3_Rev12_LAST.sds ├── RT3_Rev12_LAST.ssp ├── RT3_Rev12_LAST.suf ├── RT3_Rev12_LAST.tis ├── RT3_Tat10.fa ├── RT3_Tat11.fa ├── RT3_Tat13.fa ├── RT3_Tat15.fa ├── RT3_Tat16.fa ├── RT3_sORF1.fa ├── RT3_sORF1.fa.fai ├── RT3_sORF1_LAST.bck ├── RT3_sORF1_LAST.des ├── RT3_sORF1_LAST.prj ├── RT3_sORF1_LAST.sds ├── RT3_sORF1_LAST.ssp ├── RT3_sORF1_LAST.suf ├── RT3_sORF1_LAST.tis ├── RT3_sORF3.fa ├── RT3_sORF3.fa.fai ├── RT3_sORF3_LAST.bck ├── RT3_sORF3_LAST.des ├── RT3_sORF3_LAST.prj ├── RT3_sORF3_LAST.sds ├── RT3_sORF3_LAST.ssp ├── RT3_sORF3_LAST.suf └── RT3_sORF3_LAST.tis /.gitignore: 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