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/usr/share/cct/lib/scripts/assign_cogs/sample_output/sample_1.gff
/usr/share/cct/lib/scripts/assign_cogs/sample_output/sample_1b.gff
/usr/share/cct/lib/scripts/assign_cogs/sample_output/sample_2.gff
/usr/share/cct/lib/scripts/assign_cogs/sample_output/sample_2b.gff
/usr/share/cct/lib/scripts/assign_cogs/test_input/sample_1.gbk
/usr/share/cct/lib/scripts/assign_cogs/test_input/sample_2.fna
/usr/share/cct/lib/scripts/cgview_xml_builder/test_input/R_denitrificans.cogs
/usr/share/cct/lib/scripts/cgview_xml_builder/test_input/R_denitrificans.gbk
/usr/share/cct/lib/scripts/cgview_xml_builder/test_input/labels_to_show.txt
/usr/share/cct/lib/scripts/cgview_xml_builder/test_input/prokka_multicontig.gbk
/usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_multiple_chromosomes_20
/usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_multiple_chromosomes_20.tab
/usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_multiple_chromosomes_21
/usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_multiple_chromosomes_21.tab
/usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_single_chromosome_20
/usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_single_chromosome_20.tab
/usr/share/cct/lib/scripts/convert_vcf_to_features/test_input/input_multiple_chromosomes.vcf
/usr/share/cct/lib/scripts/convert_vcf_to_features/test_input/input_single_chromosome.vcf
/usr/share/cct/lib/scripts/get_cds/sample_output/R_denitrificans.cds.faa
/usr/share/cct/lib/scripts/get_cds/sample_output/R_denitrificans.cds.fna
/usr/share/cct/lib/scripts/get_cds/sample_output/prokka_multicontig.cds.faa
/usr/share/cct/lib/scripts/get_cds/sample_output/prokka_multicontig.cds.fna
/usr/share/cct/lib/scripts/get_cds/test_input/R_denitrificans.gbk
/usr/share/cct/lib/scripts/get_cds/test_input/prokka_multicontig.gbk
/usr/share/cct/lib/scripts/get_orfs/sample_output/R_denitrificans.orfs.faa
/usr/share/cct/lib/scripts/get_orfs/sample_output/R_denitrificans.orfs.fna
/usr/share/cct/lib/scripts/get_orfs/sample_output/prokka_multicontig.orfs.faa
/usr/share/cct/lib/scripts/get_orfs/sample_output/prokka_multicontig.orfs.fna
/usr/share/cct/lib/scripts/get_orfs/test_input/R_denitrificans.gbk
/usr/share/cct/lib/scripts/get_orfs/test_input/prokka_multicontig.gbk
/usr/share/cct/lib/scripts/local_blast_client/sample_output/results_blastn.txt
/usr/share/cct/lib/scripts/local_blast_client/sample_output/results_blastp.txt
/usr/share/cct/lib/scripts/local_blast_client/sample_output/results_blastx.txt
/usr/share/cct/lib/scripts/local_blast_client/sample_output/results_tblastn.txt
/usr/share/cct/lib/scripts/local_blast_client/sample_output/results_tblastx.txt
/usr/share/cct/lib/scripts/local_blast_client/test_input/test_dna_database.fasta
/usr/share/cct/lib/scripts/local_blast_client/test_input/test_input_dna.fasta
/usr/share/cct/lib/scripts/local_blast_client/test_input/test_input_protein.fasta
/usr/share/cct/lib/scripts/local_blast_client/test_input/test_protein_database.fasta
/usr/share/cct/lib/scripts/ncbi_search/sample_output/NC_009933.gbk
/usr/share/cct/lib/scripts/ncbi_search/sample_output/NC_009934.gbk
/usr/share/cct/lib/scripts/ncbi_search/sample_output/combined.gbk
/usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/output1.fasta
/usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/output2.fasta
/usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/output3.fasta
/usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq.fasta
/usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq_multi.fasta
/usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq_multi_s100_v5.fasta
/usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq_multi_v5.fasta
/usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq_s100_v5.fasta
/usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq_v5.fasta
/usr/share/cct/lib/scripts/sequence_to_multi_fasta/test_input/test_seq.fasta
/usr/share/cct/lib/scripts/sequence_to_multi_fasta/test_input/test_seq_multi.fasta
/usr/share/cct/test_projects/test_blastn/comparison_genomes/match_end_of_orf.fasta
/usr/share/cct/test_projects/test_blastn/comparison_genomes/match_end_of_orf_rev_comp.fasta
/usr/share/cct/test_projects/test_blastn/comparison_genomes/match_start_of_orf.fasta
/usr/share/cct/test_projects/test_blastn/comparison_genomes/match_start_of_orf_rev_comp.fasta
/usr/share/cct/test_projects/test_blastn/project_settings.conf
/usr/share/cct/test_projects/test_blastn/reference_genome/two_copies_of_long_ORF_opposite_directions.fasta
/usr/share/cct/test_projects/test_blastp/comparison_genomes/match_end_of_orf.fasta
/usr/share/cct/test_projects/test_blastp/comparison_genomes/match_start_of_orf.fasta
/usr/share/cct/test_projects/test_blastp/project_settings.conf
/usr/share/cct/test_projects/test_blastp/reference_genome/two_copies_of_long_ORF_opposite_directions.fasta
/usr/share/cct/test_projects/test_blastx/comparison_genomes/match_end_of_orf.fasta
/usr/share/cct/test_projects/test_blastx/comparison_genomes/match_start_of_orf.fasta
/usr/share/cct/test_projects/test_blastx/project_settings.conf
/usr/share/cct/test_projects/test_blastx/reference_genome/two_copies_of_long_ORF_opposite_directions.fasta
/usr/share/cct/test_projects/test_orfs/project_settings.conf
/usr/share/cct/test_projects/test_orfs/reference_genome/random.fasta
/usr/share/cct/test_projects/test_plots/project_settings.conf
/usr/share/cct/test_projects/test_plots/reference_genome/test.fasta
/usr/share/cct/test_projects/test_tblastn/comparison_genomes/match_end_of_orf.fasta
/usr/share/cct/test_projects/test_tblastn/comparison_genomes/match_end_of_orf_rev_comp.fasta
/usr/share/cct/test_projects/test_tblastn/comparison_genomes/match_start_of_orf.fasta
/usr/share/cct/test_projects/test_tblastn/comparison_genomes/match_start_of_orf_rev_comp.fasta
/usr/share/cct/test_projects/test_tblastn/project_settings.conf
/usr/share/cct/test_projects/test_tblastn/reference_genome/two_copies_of_long_ORF_opposite_directions.fasta
/usr/share/cct/test_projects/test_tblastx/comparison_genomes/match_end_of_orf.fasta
/usr/share/cct/test_projects/test_tblastx/comparison_genomes/match_end_of_orf_rev_comp.fasta
/usr/share/cct/test_projects/test_tblastx/comparison_genomes/match_start_of_orf.fasta
/usr/share/cct/test_projects/test_tblastx/comparison_genomes/match_start_of_orf_rev_comp.fasta
/usr/share/cct/test_projects/test_tblastx/project_settings.conf
/usr/share/cct/test_projects/test_tblastx/reference_genome/two_copies_of_long_ORF_opposite_directions.fasta
/usr/share/doc/cct-examples/changelog.Debian.gz
/usr/share/doc/cct-examples/copyright
/usr/share/doc/cct/examples/sample_projects/sample_project_1/comparison_genomes/NC_007717.gbk.gz
/usr/share/doc/cct/examples/sample_projects/sample_project_1/comparison_genomes/NC_007718.gbk.gz
/usr/share/doc/cct/examples/sample_projects/sample_project_1/comparison_genomes/NC_007720.gbk.gz
/usr/share/doc/cct/examples/sample_projects/sample_project_1/labels_to_show.txt
/usr/share/doc/cct/examples/sample_projects/sample_project_1/project_settings_a.conf
/usr/share/doc/cct/examples/sample_projects/sample_project_1/project_settings_b.conf
/usr/share/doc/cct/examples/sample_projects/sample_project_1/project_settings_c.conf
/usr/share/doc/cct/examples/sample_projects/sample_project_1/reference_genome/NC_007719.gbk.gz
/usr/share/doc/cct/examples/sample_projects/sample_project_2/comparison_genomes/Methanococcus_maripaludis.gbk.gz
/usr/share/doc/cct/examples/sample_projects/sample_project_2/comparison_genomes/Methanosarcina_acetivorans.gbk.gz
/usr/share/doc/cct/examples/sample_projects/sample_project_2/comparison_genomes/Thermococcus_kodakaraensis.gbk.gz
/usr/share/doc/cct/examples/sample_projects/sample_project_2/project_settings_a.conf
/usr/share/doc/cct/examples/sample_projects/sample_project_2/project_settings_b.conf
/usr/share/doc/cct/examples/sample_projects/sample_project_2/project_settings_c.conf
/usr/share/doc/cct/examples/sample_projects/sample_project_2/reference_genome/Methanobacterium_thermoautotrophicum.gbk.gz
/usr/share/doc/cct/examples/sample_projects/sample_project_3/comparison_genomes/NC_000913.gbk.gz
/usr/share/doc/cct/examples/sample_projects/sample_project_3/project_settings_a.conf
/usr/share/doc/cct/examples/sample_projects/sample_project_3/project_settings_b.conf
/usr/share/doc/cct/examples/sample_projects/sample_project_3/project_settings_c.conf
/usr/share/doc/cct/examples/sample_projects/sample_project_3/reference_genome/NC_004463.gbk.gz
/usr/share/doc/cct/examples/sample_projects/sample_project_4/analysis/analysis_1.gff
/usr/share/doc/cct/examples/sample_projects/sample_project_4/analysis/analysis_2.gff
/usr/share/doc/cct/examples/sample_projects/sample_project_4/comparison_genomes/L09136.gbk.gz
/usr/share/doc/cct/examples/sample_projects/sample_project_4/comparison_genomes/L09137.gbk.gz
/usr/share/doc/cct/examples/sample_projects/sample_project_4/features/features_1.gff
/usr/share/doc/cct/examples/sample_projects/sample_project_4/features/features_2.gff
/usr/share/doc/cct/examples/sample_projects/sample_project_4/project_settings_a.conf
/usr/share/doc/cct/examples/sample_projects/sample_project_4/project_settings_b.conf
/usr/share/doc/cct/examples/sample_projects/sample_project_4/project_settings_c.conf
/usr/share/doc/cct/examples/sample_projects/sample_project_4/reference_genome/X52329.gbk.gz
/usr/share/doc/cct/examples/sample_projects/sample_project_5/comparison_genomes/Arabidopsis_mito.gbk.gz
/usr/share/doc/cct/examples/sample_projects/sample_project_5/comparison_genomes/E_coli.gbk.gz
/usr/share/doc/cct/examples/sample_projects/sample_project_5/comparison_genomes/Human_mito.gbk.gz
/usr/share/doc/cct/examples/sample_projects/sample_project_5/project_settings_a.conf
/usr/share/doc/cct/examples/sample_projects/sample_project_5/project_settings_b.conf
/usr/share/doc/cct/examples/sample_projects/sample_project_5/project_settings_c.conf
/usr/share/doc/cct/examples/sample_projects/sample_project_5/reference_genome/NC_001823.gbk.gz
/usr/share/doc/cct/examples/sample_projects/sample_project_6/comparison_genomes/fem.fasta
/usr/share/doc/cct/examples/sample_projects/sample_project_6/project_settings_a.conf
/usr/share/doc/cct/examples/sample_projects/sample_project_6/project_settings_b.conf
/usr/share/doc/cct/examples/sample_projects/sample_project_6/project_settings_c.conf
/usr/share/doc/cct/examples/sample_projects/sample_project_6/reference_genome/ref.fas.gz
/usr/share/doc/cct/examples/test_projects
/usr/share/doc/cct/run-unit-test