O:\DEJAVNOSTI\OMIKE\pISA-Projects\_p_stRT 
Folder PATH listing for volume Skupni
Volume serial number is 8EBF-0990
O:.
|   common.ini
|   d.tmp
|   FST.txt
|   makeInvestigation.bat
|   Metadata_files.md
|   meta_I_Template.txt
|   README.MD
|   showMetadata.bat
|   showTree.bat
|   t.tmp
|   TREE.TXT
|   xcheckMetadata.bat
|   xCheckMetadata.md
|   _PROJECT_METADATA.TXT
|   _p_stRT_TREE.TXT
|   
+---presentations
|       README.MD
|       
+---reports
|       README.MD
|       
\---_I_STRT
    |   common.ini
    |   makeStudy.bat
    |   meta_S_Template.txt
    |   phenodata_20191022.txt
    |   README.MD
    |   showMetadata.bat
    |   showTree.bat
    |   xcheckMetadata.bat
    |   _INVESTIGATION_METADATA.TXT
    |   
    +---presentations
    |       README.MD
    |       
    +---reports
    |       README.MD
    |       
    +---_S_01_sequences
    |   |   common.ini
    |   |   makeAssay.bat
    |   |   meta_A_Template.txt
    |   |   README.MD
    |   |   showMetadata.bat
    |   |   showTree.bat
    |   |   xcheckMetadata.bat
    |   |   _STUDY_METADATA.TXT
    |   |   
    |   \---reports
    |           README.MD
    |           SupplementaryTableS1-Input_sequences_information.xlsx
    |           
    +---_S_02_denovo
    |   |   common.ini
    |   |   makeAssay.bat
    |   |   meta_A_Template.txt
    |   |   README.MD
    |   |   showMetadata.bat
    |   |   showTree.bat
    |   |   xcheckMetadata.bat
    |   |   _STUDY_METADATA.TXT
    |   |   
    |   \---reports
    |           README.MD
    |           SupplementaryTableS2-Primary_potato_transcriptome_assemblies.xlsx
    |           
    +---_S_03_stCuSTr
    |   |   common.ini
    |   |   makeAssay.bat
    |   |   meta_A_Template.txt
    |   |   README.MD
    |   |   showMetadata.bat
    |   |   showTree.bat
    |   |   xcheckMetadata.bat
    |   |   _STUDY_METADATA.TXT
    |   |   
    |   +---reports
    |   |       README.MD
    |   |       
    |   +---_A_01_evigene
    |   |   |   intermediate_tr2aacds_Desiree.tar.gz
    |   |   |   intermediate_tr2aacds_PW363.tar.gz.aa
    |   |   |   intermediate_tr2aacds_PW363.tar.gz.ab
    |   |   |   intermediate_tr2aacds_Rywal.tar.gz
    |   |   |   README.MD
    |   |   |   showMetadata.bat
    |   |   |   showTree.bat
    |   |   |   xcheckMetadata.bat
    |   |   |   _Assay_METADATA.TXT
    |   |   |   
    |   |   +---input
    |   |   |       path_to_files.txt
    |   |   |       
    |   |   +---output
    |   |   |       3cvs_aa.fasta.gz
    |   |   |       3cvs_cds.fasta.gz
    |   |   |       3cvs_tr.fasta.gz
    |   |   |       
    |   |   \---scripts
    |   |           01_run_commands.sh
    |   |           my_tr2aacds.sh
    |   |           README.MD
    |   |           run_tr2aacds.sh
    |   |           
    |   +---_A_02.1_BUSCO
    |   |   |   README.MD
    |   |   |   showMetadata.bat
    |   |   |   showTree.bat
    |   |   |   xcheckMetadata.bat
    |   |   |   _Assay_METADATA.TXT
    |   |   |   
    |   |   +---input
    |   |   |       path_to_files.txt
    |   |   |       
    |   |   +---output
    |   |   |       Desiree_assemblies.txt
    |   |   |       Desiree_repAlt.txt
    |   |   |       PW363_assemblies.txt
    |   |   |       PW363_repAlt.txt
    |   |   |       Rywal_assemblies.txt
    |   |   |       Rywal_rep.aa.txt
    |   |   |       Rywal_rep.tr.txt
    |   |   |       Rywal_repAlt.txt
    |   |   |       
    |   |   \---scripts
    |   |           00_get_tools_and_export_paths.txt
    |   |           01_run_BUSCO.sh
    |   |           README.MD
    |   |           
    |   +---_A_02.2_assembly-contribution-count
    |   |   |   intermediate_Desiree.tar.gz
    |   |   |   intermediate_PW363.tar.gz
    |   |   |   intermediate_Rywal.tar.gz
    |   |   |   README.MD
    |   |   |   showMetadata.bat
    |   |   |   showTree.bat
    |   |   |   xcheckMetadata.bat
    |   |   |   _Assay_METADATA.TXT
    |   |   |   
    |   |   +---input
    |   |   |       path_to_files.txt
    |   |   |       
    |   |   +---output
    |   |   |       Desiree_cnt_assemblies.txt
    |   |   |       PW363_cnt_assemblies.txt
    |   |   |       Rywal_cnt_assemblies.txt
    |   |   |       
    |   |   +---reports
    |   |   |       Figure3.pdf
    |   |   |       SupplementaryFigure1.pdf
    |   |   |       SupplementaryFigure2.pdf
    |   |   |       
    |   |   \---scripts
    |   |           countDesiree.sh
    |   |           countPW363.sh
    |   |           countRywal.sh
    |   |           
    |   +---_A_02.3_InterProScan
    |   |   |   README.MD
    |   |   |   showMetadata.bat
    |   |   |   showTree.bat
    |   |   |   xcheckMetadata.bat
    |   |   |   _Assay_METADATA.TXT
    |   |   |   
    |   |   +---input
    |   |   |       path_to_files.txt
    |   |   |       
    |   |   +---intermediate
    |   |   |   +---Desiree_IPS
    |   |   |   |       all.okalt.aa.tsv
    |   |   |   |       all.okay.aa.tsv
    |   |   |   |       
    |   |   |   +---PW363_IPS
    |   |   |   |       all.okalt.aa.tsv
    |   |   |   |       all.okay.aa.tsv
    |   |   |   |       
    |   |   |   \---Rywal_IPS
    |   |   |           all.okalt.aa.tsv
    |   |   |           all.okay.aa.tsv
    |   |   |           
    |   |   +---output
    |   |   |       Desiree_IPS_filtered_aggregated_filtered.tsv
    |   |   |       PW363_IPS_filtered_aggregated_filtered.tsv
    |   |   |       Rywal_IPS_filtered_aggregated_filtered.tsv
    |   |   |       
    |   |   +---reports
    |   |   |       IPS_PowerQuery_PivotTable.xlsx
    |   |   |       
    |   |   \---scripts
    |   |           01_potato_tr_evigene_IPS_commands.txt
    |   |           02_reshape_merge_aggregate_filter.Rmd
    |   |           
    |   +---_A_02.4_STAR
    |   |   |   README.MD
    |   |   |   showMetadata.bat
    |   |   |   showTree.bat
    |   |   |   xcheckMetadata.bat
    |   |   |   _Assay_METADATA.TXT
    |   |   |   
    |   |   +---input
    |   |   |       path_to_files.txt
    |   |   |       
    |   |   +---output
    |   |   |       output_STAR_logs-n-SJ.tar.gz
    |   |   |       
    |   |   \---scripts
    |   |           STAR_commands.txt
    |   |           
    |   +---_A_02.5_STARlong_matchAnnot
    |   |   |   README.MD
    |   |   |   showMetadata.bat
    |   |   |   showTree.bat
    |   |   |   xcheckMetadata.bat
    |   |   |   _Assay_METADATA.TXT
    |   |   |   
    |   |   +---input
    |   |   |       path_to_files.txt
    |   |   |       
    |   |   +---output
    |   |   |       output_1_STARlong-logs-n-SJ.tar.gz
    |   |   |       output_2_matchAnnot-parsed-txt.tar.gz
    |   |   |       README.MD
    |   |   |       
    |   |   \---scripts
    |   |           STARlongMatchAnnot_commands_ENCODE_denovo_param.txt
    |   |           
    |   +---_A_02.6_TransRate
    |   |   |   README.MD
    |   |   |   showMetadata.bat
    |   |   |   showTree.bat
    |   |   |   xcheckMetadata.bat
    |   |   |   _Assay_METADATA.TXT
    |   |   |   
    |   |   +---input
    |   |   |       path_to_files.txt
    |   |   |       
    |   |   +---output
    |   |   |       Desiree_initial_transrate_usingReference.log
    |   |   |       Desiree_initial_transrate_usingReference_assemblies.csv
    |   |   |       PW363_initial_transrate_usingReference.log
    |   |   |       PW363_initial_transrate_usingReference_assemblies.csv
    |   |   |       Rywal_initial_transrate_usingReference.log
    |   |   |       Rywal_initial_transrate_usingReference_assemblies.csv
    |   |   |       
    |   |   \---scripts
    |   |           run_TransRate_commands.sh
    |   |           Transrate_GitHub_README.md
    |   |           
    |   +---_A_02.7_VecScreen
    |   |   |   intermediate.tar.gz
    |   |   |   README.MD
    |   |   |   showMetadata.bat
    |   |   |   showTree.bat
    |   |   |   xcheckMetadata.bat
    |   |   |   _Assay_METADATA.TXT
    |   |   |   
    |   |   +---input
    |   |   |       path_to_files.txt
    |   |   |       
    |   |   +---output
    |   |   |       Desiree_vecscreen.tsv
    |   |   |       PW363_vecscreen.tsv
    |   |   |       Rywal_vecscreen.tsv
    |   |   |       
    |   |   \---scripts
    |   |           01_get_input.sh
    |   |           02_VecScreenPlus_blastn.sh
    |   |           ENCH_sumablastplus.pl
    |   |           
    |   +---_A_02.8_DIAMOND
    |   |   |   README.MD
    |   |   |   showMetadata.bat
    |   |   |   showTree.bat
    |   |   |   xcheckMetadata.bat
    |   |   |   _Assay_METADATA.TXT
    |   |   |   
    |   |   +---input
    |   |   |       path_to_files.txt
    |   |   |       
    |   |   +---output
    |   |   |       Desiree.cds_Solanaceae.out.ENCHformat_top1.tsv.gz
    |   |   |       Desiree.cds_solanumTuberosum.out.ENCHformat_top1.tsv.gz
    |   |   |       Desiree.cds_SP_TrEMBL_plants.out.ENCHformat_top1.tsv.gz
    |   |   |       Desiree.cds_SwissProt_TrEMBL.out.ENCHformat_top1.tsv.gz
    |   |   |       Desiree.tr_Solanaceae.out.ENCHformat_top1.tsv.gz
    |   |   |       Desiree.tr_solanumTuberosum.out.ENCHformat_top1.tsv.gz
    |   |   |       Desiree.tr_SP_TrEMBL_plants.out.ENCHformat_top1.tsv.gz
    |   |   |       Desiree.tr_SwissProt_TrEMBL.out.ENCHformat_top1.tsv.gz
    |   |   |       Desiree_rescued.tr_Solanaceae.out.ENCHformat_top1.tsv.gz
    |   |   |       Desiree_rescued.tr_solanumTuberosum.out.ENCHformat_top1.tsv.gz
    |   |   |       Desiree_rescued.tr_sprot_trembl.out.ENCHformat_top1.tsv.gz
    |   |   |       Desiree_rescued.tr_SP_TrEMBL_plants.out.ENCHformat_top1.tsv.gz
    |   |   |       PW363.cds_Solanaceae.out.ENCHformat_top1.tsv.gz
    |   |   |       PW363.cds_solanumTuberosum.out.ENCHformat_top1.tsv.gz
    |   |   |       PW363.cds_SP_TrEMBL_plants.out.ENCHformat_top1.tsv.gz
    |   |   |       PW363.cds_SwissProt_TrEMBL.out.ENCHformat_top1.tsv.gz
    |   |   |       PW363.tr_Solanaceae.out.ENCHformat_top1.tsv.gz
    |   |   |       PW363.tr_solanumTuberosum.out.ENCHformat_top1.tsv.gz
    |   |   |       PW363.tr_SP_TrEMBL_plants.out.ENCHformat_top1.tsv.gz
    |   |   |       PW363.tr_SwissProt_TrEMBL.out.ENCHformat_top1.tsv.gz
    |   |   |       PW363_rescued.tr_Solanaceae.out.ENCHformat_top1.tsv.gz
    |   |   |       PW363_rescued.tr_solanumTuberosum.out.ENCHformat_top1.tsv.gz
    |   |   |       PW363_rescued.tr_sprot_trembl.out.ENCHformat_top1.tsv.gz
    |   |   |       PW363_rescued.tr_SP_TrEMBL_plants.out.ENCHformat_top1.tsv.gz
    |   |   |       Rywal.cds_Solanaceae.out.ENCHformat_top1.tsv.gz
    |   |   |       Rywal.cds_solanumTuberosum.out.ENCHformat_top1.tsv.gz
    |   |   |       Rywal.cds_sprot_trembl.out.ENCHformat_top1.tsv.gz
    |   |   |       Rywal.cds_Swissprot_TrEMBL_plants.out.ENCHformat_top1.tsv.gz
    |   |   |       Rywal.tr_Solanaceae.out.ENCHformat_top1.tsv.gz
    |   |   |       Rywal.tr_solanumTuberosum.out.ENCHformat_top1.tsv.gz
    |   |   |       Rywal.tr_sprot_trembl.out.ENCHformat_top1.tsv.gz
    |   |   |       Rywal.tr_Swissprot_TrEMBL_plants.out.ENCHformat_top1.tsv.gz
    |   |   |       Rywal_rescued.tr_Solanaceae.out.ENCHformat_top1.tsv.gz
    |   |   |       Rywal_rescued.tr_solanumTuberosum.out.ENCHformat_top1.tsv.gz
    |   |   |       Rywal_rescued.tr_sprot_trembl.out.ENCHformat_top1.tsv.gz
    |   |   |       Rywal_rescued.tr_SP_TrEMBL_plants.out.ENCHformat_top1.tsv.gz
    |   |   |       
    |   |   \---scripts
    |   |           01_get_input.sh
    |   |           02_DIAMOND_commands.sh
    |   |           03_archive_files.sh
    |   |           
    |   +---_A_03.1_filtering
    |   |   |   README.MD
    |   |   |   showMetadata.bat
    |   |   |   showTree.bat
    |   |   |   xcheckMetadata.bat
    |   |   |   _Assay_METADATA.TXT
    |   |   |   
    |   |   +---input
    |   |   |       path_to_files.txt
    |   |   |       
    |   |   +---intermediate
    |   |   |       intermediate-2-validate-removal.tar.gz
    |   |   |       
    |   |   +---output
    |   |   |   |   Desiree_tr.cds.tsv.gz
    |   |   |   |   PW363_tr.cds.tsv.gz
    |   |   |   |   Rywal_tr.cds.tsv.gz
    |   |   |   |   
    |   |   |   \---other
    |   |   |           output_full.tar.gz
    |   |   |           output_summary.tar.gz
    |   |   |           
    |   |   +---reports
    |   |   |       03.1_Rywal_combo_withFiltering.html
    |   |   |       03.2_PW363_combo_withFiltering.html
    |   |   |       03.3_Desiree_combo_withFiltering.html
    |   |   |       
    |   |   \---scripts
    |   |           01_ID_length_pairs.sh
    |   |           02_get_otherFiles.sh
    |   |           03.1_Rywal_combo_withFiltering.Rmd
    |   |           03.2_PW363_combo_withFiltering.Rmd
    |   |           03.3_Desiree_combo_withFiltering.Rmd
    |   |           04_summary.sh
    |   |           05_validate_removal.sh
    |   |           06_archive_files.sh
    |   |           
    |   +---_A_03.2_components
    |   |   |   intermediate_4_cdhit-2d.tar.gz
    |   |   |   README.MD
    |   |   |   showMetadata.bat
    |   |   |   showTree.bat
    |   |   |   xcheckMetadata.bat
    |   |   |   _Assay_METADATA.TXT
    |   |   |   
    |   |   +---input
    |   |   |       README.MD
    |   |   |       
    |   |   +---output
    |   |   |   |   3cv_cdhit-2d_weak-components.txt.gz
    |   |   |   |   3cv_cdhit-2d_weak-components_alias.txt.gz
    |   |   |   |   fasta_3A_utrorfs-per-cv.tar.gz
    |   |   |   |   fasta_3B_eliminated-per-cv.tar.gz
    |   |   |   |   README.MD
    |   |   |   |   
    |   |   |   +---fasta_1A_rep-per-cv
    |   |   |   |       stCuSTr-D_aa_representatives.fasta.gz
    |   |   |   |       stCuSTr-D_cds_representatives.fasta.gz
    |   |   |   |       stCuSTr-D_tr_representatives.fasta.gz
    |   |   |   |       stCuSTr-P_aa_representatives.fasta.gz
    |   |   |   |       stCuSTr-P_cds_representatives.fasta.gz
    |   |   |   |       stCuSTr-P_tr_representatives.fasta.gz
    |   |   |   |       stCuSTr-R_aa_representatives.fasta.gz
    |   |   |   |       stCuSTr-R_cds_representatives.fasta.gz
    |   |   |   |       stCuSTr-R_tr_representatives.fasta.gz
    |   |   |   |       
    |   |   |   +---fasta_1B_alt-per-cv
    |   |   |   |       stCuSTr-D_aa_alternatives.fasta.gz
    |   |   |   |       stCuSTr-D_cds_alternatives.fasta.gz
    |   |   |   |       stCuSTr-D_tr_alternatives.fasta.gz
    |   |   |   |       stCuSTr-P_aa_alternatives.fasta.gz
    |   |   |   |       stCuSTr-P_cds_alternatives.fasta.gz
    |   |   |   |       stCuSTr-P_tr_alternatives.fasta.gz
    |   |   |   |       stCuSTr-R_aa_alternatives.fasta.gz
    |   |   |   |       stCuSTr-R_cds_alternatives.fasta.gz
    |   |   |   |       stCuSTr-R_tr_alternatives.fasta.gz
    |   |   |   |       
    |   |   |   \---fasta_2_all-per-cv
    |   |   |           stCuSTr-D_aa_all.fasta.gz
    |   |   |           stCuSTr-D_cds_all.fasta.gz
    |   |   |           stCuSTr-D_tr_all.fasta.gz
    |   |   |           stCuSTr-P_aa_all.fasta.gz
    |   |   |           stCuSTr-P_cds_all.fasta.gz
    |   |   |           stCuSTr-P_tr_all.fasta.gz
    |   |   |           stCuSTr-R_aa_all.fasta.gz
    |   |   |           stCuSTr-R_cds_all.fasta.gz
    |   |   |           stCuSTr-R_tr_all.fasta.gz
    |   |   |           
    |   |   \---scripts
    |   |           i1.0_copy-to-input.txt
    |   |           i1.1_parse-filtered-lists.pl
    |   |           i1.2_parse-fasta-files-pt1.pl
    |   |           i1.2_parse-fasta-files-pt2.pl
    |   |           i1.3_parse-headers.pl
    |   |           i2.1_prepare-network.pl
    |   |           i2.2_prepare-filter-master-file.pl
    |   |           i2.3_parse-n-filter-weak-components.pl
    |   |           i2.4_prepare-rep-component-table.pl
    |   |           i3.1_prepare-fastas-pt1.pl
    |   |           i3.2_prepare-fastas-pt2.pl
    |   |           i4.1_cdhit-2d.sh
    |   |           i5.1_parse-cdhit-2d.sh
    |   |           i5.2_parse-cdhit-2d-weak-components.Rmd
    |   |           i5.3_prepare-fastas.sh
    |   |           
    |   +---_A_04_TransRate
    |   |   |   README.MD
    |   |   |   showMetadata.bat
    |   |   |   showTree.bat
    |   |   |   xcheckMetadata.bat
    |   |   |   _Assay_METADATA.TXT
    |   |   |   
    |   |   +---input
    |   |   |       path_to_files.txt
    |   |   |       
    |   |   +---output
    |   |   |       Desiree_transrate_usingReference.log
    |   |   |       Desiree_transrate_usingReference_assemblies.csv
    |   |   |       PW363_transrate_usingReference.log
    |   |   |       PW363_transrate_usingReference_assemblies.csv
    |   |   |       Rywal_transrate_usingReference.log
    |   |   |       Rywal_transrate_usingReference_assemblies.csv
    |   |   |       
    |   |   \---scripts
    |   |           run_TransRate_commands.sh
    |   |           
    |   \---_A_05_BUSCO
    |       |   README.MD
    |       |   showMetadata.bat
    |       |   showTree.bat
    |       |   xcheckMetadata.bat
    |       |   _Assay_METADATA.TXT
    |       |   
    |       +---input
    |       |       path_to_files.txt
    |       |       
    |       +---output
    |       |       BUSCOall_embryophyta_odb9.tsv
    |       |       short_summary.tar
    |       |       
    |       +---scripts
    |       |       run_BUSCO_commands.sh
    |       |       
    |       \---transfer
    |               evg_out.tsv
    |               
    \---_S_04_stPanTr
        |   common.ini
        |   makeAssay.bat
        |   meta_A_Template.txt
        |   README.MD
        |   showMetadata.bat
        |   showTree.bat
        |   xcheckMetadata.bat
        |   _STUDY_METADATA.TXT
        |   
        +---reports
        |       README.MD
        |       
        +---_A_01_evigene_1_3cvs-gffmerged
        |   |   README.MD
        |   |   showMetadata.bat
        |   |   showTree.bat
        |   |   xcheckMetadata.bat
        |   |   _Assay_METADATA.TXT
        |   |   
        |   +---input
        |   |       path_to_files.txt
        |   |       StPGSC4.04n_PGSC-ITAG-merged_representative-transcript_genes_2019-04-23.gtf.gz
        |   |       StPGSC4.04n_seq_3_PGSC-c-rep_ITAG-cds_gff-2019-04-23.fasta.gz
        |   |       
        |   +---output
        |   |   |   2019-08-05_3cv_gffmerged_cds_tr2ac1_log.txt.gz
        |   |   |   3cv_gffmerged_cds.tr2aacds.log.gz
        |   |   |   3cv_gffmerged_cds.trclass.gz
        |   |   |   3cv_gffmerged_cds.trclass.sum.txt.gz
        |   |   |   
        |   |   +---dropset
        |   |   |       3cv_gffmerged_cds.drop.aa.gz
        |   |   |       3cv_gffmerged_cds.drop.cds.gz
        |   |   |       3cv_gffmerged_cds.drop.fasta.gz
        |   |   |       
        |   |   +---inputset
        |   |   |       3cv_gffmerged_cds.aa.gz
        |   |   |       3cv_gffmerged_cds.aa.qual.gz
        |   |   |       3cv_gffmerged_cds.cds.gz
        |   |   |       
        |   |   +---okayset
        |   |   |       3cv_gffmerged_cds.okalt.aa.gz
        |   |   |       3cv_gffmerged_cds.okalt.cds.gz
        |   |   |       3cv_gffmerged_cds.okalt.fasta.gz
        |   |   |       3cv_gffmerged_cds.okay.aa.gz
        |   |   |       3cv_gffmerged_cds.okay.cds.gz
        |   |   |       3cv_gffmerged_cds.okay.fasta.gz
        |   |   |       
        |   |   \---retrieve
        |   |           diff.aa.IDs.txt.gz
        |   |           diff.cds.IDs.txt.gz
        |   |           diff.tr.IDs.txt.gz
        |   |           
        |   \---scripts
        |           01_run_3cv_gffmerged_cds_commands.sh
        |           my_tr2aacds.sh
        |           README.MD
        |           run_tr2aacds.sh
        |           
        +---_A_02_components_1_3cvs-gffmerged
        |   |   README.MD
        |   |   showMetadata.bat
        |   |   showTree.bat
        |   |   xcheckMetadata.bat
        |   |   _Assay_METADATA.TXT
        |   |   
        |   +---input
        |   |       3cvs_sequences_keep.txt.gz
        |   |       pantr_aa.fasta.gz
        |   |       pantr_cds.fasta.gz
        |   |       pantr_tr.fasta.gz
        |   |       phureja_sequences_keep.txt.gz
        |   |       
        |   +---output
        |   |       stPanTr_aa_alternatives.fasta.gz
        |   |       stPanTr_aa_representatives.fasta.gz
        |   |       stPanTr_cds_alternatives.fasta.gz
        |   |       stPanTr_cds_representatives.fasta.gz
        |   |       stPanTr_tr_alternatives.fasta.gz
        |   |       stPanTr_tr_representatives.fasta.gz
        |   |       
        |   +---reports
        |   \---scripts
        |           i1.0_copy-to-input.txt
        |           i1.2_parse-fasta-files-pt1.pl
        |           i1.2_parse-fasta-files-pt2.pl
        |           i1.3_parse-headers.pl
        |           i2.1_prepare-network.pl
        |           i2.3_parse-weak-components.pl
        |           i2.4_prepare-rep-component-table.pl
        |           i3.1_prepare-fastas-pt1.pl
        |           i4.1_compress-fastas.sh
        |           
        +---_A_03_BUSCO_1_3cvs-gffmerged
        |   |   README.MD
        |   |   showMetadata.bat
        |   |   showTree.bat
        |   |   xcheckMetadata.bat
        |   |   _Assay_METADATA.TXT
        |   |   
        |   +---input
        |   |       path_to_files.txt
        |   |       
        |   +---output
        |   |       BUSCO_stPanTr_embryophyta_odb9.tsv
        |   |       short_summary.tar
        |   |       
        |   \---scripts
        |           run_BUSCO_commands.sh
        |           
        +---_A_04-MSA
        |   |   README.MD
        |   |   showMetadata.bat
        |   |   showTree.bat
        |   |   xcheckMetadata.bat
        |   |   _Assay_METADATA.TXT
        |   |   
        |   +---input
        |   |       D_P_R_g.tar.gz
        |   |       README.MD
        |   |       selected_4_wc.tar.gz
        |   |       
        |   +---other
        |   +---output
        |   |   |   5cv_weak-components.txt
        |   |   |   README.MD
        |   |   |   
        |   |   +---out_aa_ClustalOmega_selected_4_wc_150_off_5_28
        |   |   |       stPanTr_007290.txt.aligned
        |   |   |       stPanTr_007290.txt.aligned.mview.html
        |   |   |       stPanTr_007290.txt.fasta
        |   |   |       stPanTr_007290.txt.ph
        |   |   |       stPanTr_007290.txt_.err.txt
        |   |   |       stPanTr_007290.txt_myLog.txt
        |   |   |       stPanTr_028778.txt.aligned
        |   |   |       stPanTr_028778.txt.aligned.mview.html
        |   |   |       stPanTr_028778.txt.fasta
        |   |   |       stPanTr_028778.txt.ph
        |   |   |       stPanTr_028778.txt_.err.txt
        |   |   |       stPanTr_028778.txt_myLog.txt
        |   |   |       stPanTr_038338.txt.aligned
        |   |   |       stPanTr_038338.txt.aligned.mview.html
        |   |   |       stPanTr_038338.txt.fasta
        |   |   |       stPanTr_038338.txt.ph
        |   |   |       stPanTr_038338.txt_.err.txt
        |   |   |       stPanTr_038338.txt_myLog.txt
        |   |   |       stPanTr_079878.txt.aligned
        |   |   |       stPanTr_079878.txt.aligned.mview.html
        |   |   |       stPanTr_079878.txt.fasta
        |   |   |       stPanTr_079878.txt.ph
        |   |   |       stPanTr_079878.txt_.err.txt
        |   |   |       stPanTr_079878.txt_myLog.txt
        |   |   |       
        |   |   +---out_cds_ClustalOmega_selected_4_wc_150_off_5_28
        |   |   |       stPanTr_007290.txt.aligned
        |   |   |       stPanTr_007290.txt.aligned.mview.html
        |   |   |       stPanTr_007290.txt.fasta
        |   |   |       stPanTr_007290.txt.ph
        |   |   |       stPanTr_007290.txt_.err.txt
        |   |   |       stPanTr_007290.txt_myLog.txt
        |   |   |       stPanTr_028778.txt.aligned
        |   |   |       stPanTr_028778.txt.aligned.mview.html
        |   |   |       stPanTr_028778.txt.fasta
        |   |   |       stPanTr_028778.txt.ph
        |   |   |       stPanTr_028778.txt_.err.txt
        |   |   |       stPanTr_028778.txt_myLog.txt
        |   |   |       stPanTr_038338.txt.aligned
        |   |   |       stPanTr_038338.txt.aligned.mview.html
        |   |   |       stPanTr_038338.txt.fasta
        |   |   |       stPanTr_038338.txt.ph
        |   |   |       stPanTr_038338.txt_.err.txt
        |   |   |       stPanTr_038338.txt_myLog.txt
        |   |   |       stPanTr_079878.txt.aligned
        |   |   |       stPanTr_079878.txt.aligned.mview.html
        |   |   |       stPanTr_079878.txt.fasta
        |   |   |       stPanTr_079878.txt.ph
        |   |   |       stPanTr_079878.txt_.err.txt
        |   |   |       stPanTr_079878.txt_myLog.txt
        |   |   |       
        |   |   \---out_MAFFT_D_P_R_g_full_off_20_28
        |   |           Merged.aa.html
        |   |           
        |   +---reports
        |   |       Figure4.pdf
        |   |       README.MD
        |   |       stPanTr_geneCount_paralogue-clusters.tiff
        |   |       SupplementaryFigure3.pdf
        |   |       
        |   +---scripts
        |   |       01_merge_all_wc.Rmd
        |   |       02_run_5cv.fasta_MSA.sh
        |   |       MSA.py
        |   |       print.sh
        |   |       
        |   \---testSet
        |       |   my.fasta
        |       |   
        |       \---folderWithIds
        |               IDs1
        |               IDs2
        |               
        \---_A_05_BUSCO-Stat
            |   README.MD
            |   showMetadata.bat
            |   showTree.bat
            |   xcheckMetadata.bat
            |   _Assay_METADATA.TXT
            |   
            +---input
            |       path_to_files.txt
            |       README.MD
            |       
            +---intermediate
            |       BUSCOall_embryophyta_odb9.tsv
            |       BUSCO_stPanTr_embryophyta_odb9.tsv
            |       evg_out.tsv
            |       
            +---other
            |       README.MD
            |       
            +---output
            |       README.MD
            |       
            +---reports
            |       BUSCO1.pdf
            |       BUSCO_plots.html
            |       README.MD
            |       
            \---scripts
                    BUSCO_plots.Rmd
                    README.MD