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[up]
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drwxr-xr-x |
 accessory_graphs/
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drwxr-xr-x |
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allow_no_fasta_delimiter/
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drwxr-xr-x |
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core_alignment/
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drwxr-xr-x |
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core_alignment_gene_lookup/
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drwxr-xr-x |
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genbank_gbff/
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drwxr-xr-x |
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gene_name_field/
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drwxr-xr-x |
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kraken_test/
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drwxr-xr-x |
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locus_tag_gffs/
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drwxr-xr-x |
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multifasta_files/
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drwxr-xr-x |
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pan_genome_sequences/
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drwxr-xr-x |
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post_analysis/
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drwxr-xr-x |
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post_analysis_expected/
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drwxr-xr-x |
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reformat_input_gffs/
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drwxr-xr-x |
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split_groups/
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drwxr-xr-x |
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split_pan_genome_sequences/
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drwxr-xr-x |
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unique_genes_per_sample/
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drwxr-xr-x |
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variable_core/
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drwxr-xr-x |
 blast_results
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892 |
-rw-r--r-- |
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clustered_proteins
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473 |
-rw-r--r-- |
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clustered_proteins_pan_genome
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485 |
-rw-r--r-- |
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clustered_proteins_post_analysis
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316 |
-rw-r--r-- |
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clusters_input.fa
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428 |
-rw-r--r-- |
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clusters_to_inflate
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1163 |
-rw-r--r-- |
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clusters_to_inflate.mcl
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139 |
-rw-r--r-- |
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clusters_to_inflate_original_input.fa
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728 |
-rw-r--r-- |
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clustersfile
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907 |
-rw-r--r-- |
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core_alignment.csv
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541 |
-rw-r--r-- |
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core_alignment_core0.66.csv
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542 |
-rw-r--r-- |
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core_group_statistics.csv
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1158 |
-rw-r--r-- |
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empty_file
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0 |
-rw-r--r-- |
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example_1.faa
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1561 |
-rw-r--r-- |
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example_2.faa
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1431 |
-rw-r--r-- |
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example_3.faa
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2341 |
-rw-r--r-- |
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example_annotation.gff
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20122 |
-rw-r--r-- |
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example_annotation.gff.proteome.faa.expected
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2783 |
-rw-r--r-- |
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example_annotation_2.gff
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20122 |
-rw-r--r-- |
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example_annotation_no_fasta_line.gff
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20114 |
-rw-r--r-- |
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example_groups
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213 |
-rw-r--r-- |
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example_groups_without_labels
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159 |
-rw-r--r-- |
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exp_qc_report.csv
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153 |
-rw-r--r-- |
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exp_qc_report_real.csv
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111 |
-rw-r--r-- |
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expected_0.seq
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179 |
-rw-r--r-- |
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expected_5.seq
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362 |
-rw-r--r-- |
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expected_accessory_binary_genes.fa
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40 |
-rw-r--r-- |
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expected_accessory_binary_genes_bounded.fa
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32 |
-rw-r--r-- |
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expected_clustered_proteins
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305 |
-rw-r--r-- |
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expected_clusters_to_inflate
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398 |
-rw-r--r-- |
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expected_combined_proteome.fa
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2992 |
-rw-r--r-- |
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expected_combined_proteome_with_filtering.fa
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4466 |
-rw-r--r-- |
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expected_complement_of_groups.gg
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90 |
-rw-r--r-- |
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expected_complement_of_groups_core0.66.gg
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39 |
-rw-r--r-- |
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expected_core_60_summary_statistics.txt
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193 |
-rw-r--r-- |
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expected_core_gene_alignment.aln
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52 |
-rw-r--r-- |
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expected_core_gene_alignment_core0.66.aln
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45 |
-rw-r--r-- |
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expected_create_pan_genome.fa
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2705 |
-rw-r--r-- |
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expected_example_annotation_1.faa
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3552 |
-rw-r--r-- |
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expected_filtered_original_input.fa
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584 |
-rw-r--r-- |
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expected_g2_g5_pan_genome_reference.fa
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3774 |
-rw-r--r-- |
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expected_gene_presence_and_absence.Rtab
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131 |
-rw-r--r-- |
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expected_gff_set_difference_common_set_statistics.csv
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584 |
-rw-r--r-- |
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expected_group_labels
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213 |
-rw-r--r-- |
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expected_group_statitics.csv
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969 |
-rw-r--r-- |
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expected_group_statitics_missing_genes.csv
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1020 |
-rw-r--r-- |
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expected_group_statitics_verbose.csv
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2291 |
-rw-r--r-- |
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expected_inflated_results
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339 |
-rw-r--r-- |
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expected_intersection_of_groups.gg
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21 |
-rw-r--r-- |
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expected_intersection_of_groups_core0.66.gg
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72 |
-rw-r--r-- |
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expected_intersection_of_groups_paralogs.gg
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42 |
-rw-r--r-- |
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expected_mafft_input.fa.aln
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3839 |
-rw-r--r-- |
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expected_mafft_real_data_core_gene_alignment.aln
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132166 |
-rw-r--r-- |
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expected_nnn_at_end.fa
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46 |
-rw-r--r-- |
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expected_nuc_multifasta.fa.aln
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5154 |
-rw-r--r-- |
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expected_nuc_multifasta.faa
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2179 |
-rw-r--r-- |
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expected_nuc_multifasta_mafft.fa.aln
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5145 |
-rw-r--r-- |
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expected_number_of_conserved_genes.tab
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60 |
-rw-r--r-- |
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expected_number_of_conserved_genes_0.6.tab
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60 |
-rw-r--r-- |
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expected_number_of_genes_in_pan_genome.tab
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60 |
-rw-r--r-- |
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expected_number_of_new_genes.tab
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60 |
-rw-r--r-- |
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expected_number_of_unique_genes.tab
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60 |
-rw-r--r-- |
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expected_one_gene_presence_and_absence.Rtab
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55 |
-rw-r--r-- |
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expected_out_of_order_fasta.fa.sorted.fa
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70 |
-rw-r--r-- |
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expected_output_core_missing_genes.aln
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155 |
-rw-r--r-- |
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expected_output_filtered.fa
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386 |
-rw-r--r-- |
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expected_output_groups
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196 |
-rw-r--r-- |
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expected_output_groups_cdhit
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78 |
-rw-r--r-- |
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expected_output_groups_group_2.fa
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933 |
-rw-r--r-- |
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expected_output_groups_group_2_multi.fa
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1041 |
-rw-r--r-- |
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expected_output_groups_group_5.fa
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457 |
-rw-r--r-- |
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expected_output_groups_group_5_multi.fa
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478 |
-rw-r--r-- |
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expected_output_merged.aln
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160 |
-rw-r--r-- |
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expected_output_merged_sparse.aln
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148 |
-rw-r--r-- |
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expected_pan_genome.fa
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1537 |
-rw-r--r-- |
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expected_pan_genome_one_gene_per_fasta.fa
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1736 |
-rw-r--r-- |
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expected_pan_genome_reference.fa
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82638 |
-rw-r--r-- |
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expected_prank_input.fa.aln
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3821 |
-rw-r--r-- |
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expected_query_1.fna
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15332 |
-rw-r--r-- |
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expected_query_2.fna
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15332 |
-rw-r--r-- |
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expected_real_data_core_gene_alignment.aln
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132160 |
-rw-r--r-- |
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expected_reannotated_groups_file
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98 |
-rw-r--r-- |
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expected_sample_weights_accessory_graph.dot
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248 |
-rw-r--r-- |
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expected_sample_weights_core_accessory_graph.dot
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459 |
-rw-r--r-- |
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expected_set_difference_common_set
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55 |
-rw-r--r-- |
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expected_set_difference_common_set_statistics.csv
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560 |
-rw-r--r-- |
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expected_set_difference_unique_set_one
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13 |
-rw-r--r-- |
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expected_set_difference_unique_set_one_statistics.csv
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418 |
-rw-r--r-- |
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expected_set_difference_unique_set_two
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43 |
-rw-r--r-- |
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expected_set_difference_unique_set_two_statistics.csv
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551 |
-rw-r--r-- |
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expected_some_different_output
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3513 |
-rw-r--r-- |
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expected_summary_statistics.txt
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192 |
-rw-r--r-- |
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expected_uneven_sequences.fa
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90 |
-rw-r--r-- |
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expected_union_of_groups.gg
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111 |
-rw-r--r-- |
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gene_category_count.csv
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8681 |
-rw-r--r-- |
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group_1.fa.aln
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4500 |
-rw-r--r-- |
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group_9.fa
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729 |
-rw-r--r-- |
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input_accessory_binary.fa
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1071 |
-rw-r--r-- |
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input_block_spreadsheet.csv
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10323 |
-rw-r--r-- |
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kraken_report.txt
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956 |
-rw-r--r-- |
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large_accessory_binary_genes.fa
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188536 |
-rw-r--r-- |
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mafft_input.fa
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3400 |
-rw-r--r-- |
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mcl_file
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169 |
-rw-r--r-- |
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mdoH.fa.aln
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5210 |
-rw-r--r-- |
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mdoH_mafft.fa.aln
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5210 |
-rw-r--r-- |
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multfasta1.aln
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92 |
-rw-r--r-- |
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multfasta2.aln
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100 |
-rw-r--r-- |
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multfasta3.aln
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128 |
-rw-r--r-- |
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multfasta4.aln
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67 |
-rw-r--r-- |
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multfasta5.aln
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67 |
-rw-r--r-- |
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nnn_at_end.fa
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57 |
-rw-r--r-- |
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nnn_at_end.fa.sorted.fa
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46 |
-rw-r--r-- |
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nuc_multifasta.fa
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6361 |
-rw-r--r-- |
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nuc_to_be_aligned.fa
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5138 |
-rw-r--r-- |
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out_of_order_fasta.fa
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70 |
-rw-r--r-- |
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out_of_order_fasta.fa.sorted.fa
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70 |
-rw-r--r-- |
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overall_gene_presence_absence.csv
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2946 |
-rw-r--r-- |
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prank_input.fa
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3400 |
-rw-r--r-- |
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proteome_with_and_without_descriptions.faa
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1393 |
-rw-r--r-- |
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query_1.fa
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35 |
-rw-r--r-- |
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query_1.gff
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20104 |
-rw-r--r-- |
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query_1_alternative_patterns.gff
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16609 |
-rw-r--r-- |
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query_2.fa
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35 |
-rw-r--r-- |
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query_2.gff
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20098 |
-rw-r--r-- |
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query_3.fa
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35 |
-rw-r--r-- |
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query_3.gff
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20098 |
-rw-r--r-- |
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query_4_missing_genes.fa
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8 |
-rw-r--r-- |
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query_4_missing_genes.gff
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15758 |
-rw-r--r-- |
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query_5.gff
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20098 |
-rw-r--r-- |
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query_6.gff
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20098 |
-rw-r--r-- |
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query_groups
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110 |
-rw-r--r-- |
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query_groups_all_merged
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56 |
-rw-r--r-- |
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query_groups_missing_genes
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114 |
-rw-r--r-- |
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query_groups_paralogs
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103 |
-rw-r--r-- |
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query_groups_reference
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94 |
-rw-r--r-- |
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raxml.tre
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8096 |
-rw-r--r-- |
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real_data_1.gff
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145749 |
-rw-r--r-- |
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real_data_2.gff
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145749 |
-rw-r--r-- |
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real_data_core_gene_alignment.aln
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118750 |
-rw-r--r-- |
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reorder_isolates.tre
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57 |
-rw-r--r-- |
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reorder_isolates_expected_output.csv
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777 |
-rw-r--r-- |
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reorder_isolates_expected_output_breadth_alpha.csv
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777 |
-rw-r--r-- |
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reorder_isolates_expected_output_breadth_creation.csv
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777 |
-rw-r--r-- |
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reorder_isolates_expected_output_breadth_height.csv
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777 |
-rw-r--r-- |
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reorder_isolates_expected_output_breadth_revalpha.csv
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777 |
-rw-r--r-- |
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reorder_isolates_expected_output_depth_alpha.csv
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777 |
-rw-r--r-- |
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reorder_isolates_expected_output_depth_creation.csv
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777 |
-rw-r--r-- |
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reorder_isolates_expected_output_depth_height.csv
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777 |
-rw-r--r-- |
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reorder_isolates_expected_output_depth_revalpha.csv
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777 |
-rw-r--r-- |
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reorder_isolates_input.csv
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768 |
-rw-r--r-- |
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sequences_with_unknowns.faa
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1474 |
-rw-r--r-- |
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shred1.gff
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892 |
-rw-r--r-- |
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shred1.shred.fa
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168 |
-rw-r--r-- |
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shred2.gff
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892 |
-rw-r--r-- |
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shred2.shred.fa
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168 |
-rw-r--r-- |
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sopB.fa.aln
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3460 |
-rw-r--r-- |
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speH.fa.aln
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1488 |
-rw-r--r-- |
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uneven_sequences.fa
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80 |
-rw-r--r-- |
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uneven_sequences.fa.sorted.fa
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90 |
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