bin/PIRATE
bin/PIRATE_to_Rtab.pl
bin/PIRATE_to_roary.pl
bin/analyse_blast_outputs.pl
bin/analyse_loci_list.pl
bin/annotate_treeWAS_output.pl
bin/convert_to_distmat.pl
bin/convert_to_treeWAS.pl
bin/create_pangenome_alignment_aa.pl
bin/pangenome_variants_to_treeWAS.pl
bin/paralogs_to_Rtab.pl
bin/select_representative
bin/subsample_outputs.pl
bin/subset_alignments.pl
bin/unique_sequences.pl
scripts/aa_align_to_nucleotide.pl
scripts/aggregate_erroneous_families.pl
scripts/aggregate_multigene_families.pl
scripts/align_feature_sequences.pl
scripts/align_nucleotide_sequences.pl
scripts/check_dependencies.pl
scripts/check_paralogs.pl
scripts/classify_aligned_paralogs.pl
scripts/classify_paralogs.pl
scripts/create_pangenome_alignment.pl
scripts/extract_feature_sequences.pl
scripts/feature_coordinate_extracter.pl
scripts/gene_cluster_to_binary_fasta.pl
scripts/jokes.txt
scripts/link_clusters.pl
scripts/link_clusters_runner.pl
scripts/pangenome_construction.pl
scripts/pangenome_graph.pl
scripts/parse_GFF.pl
scripts/parse_pangenomes.pl
scripts/plot_summary.R
scripts/run_PIRATE.pl
scripts/run_classify_paralogs_batch.pl
scripts/run_classify_paralogs_sequential.pl
scripts/select_representative.pl
scripts/sort_on_clusters.pl
scripts/split_paralogs.old.pl
scripts/split_paralogs.original.pl
scripts/split_paralogs.pl
scripts/split_paralogs_runner.pl
scripts/table_summary.pl
test/HO_5096_0412_test.gff
test/MRSA252_test.gff
test/Newman_test.gff
test/S0385_test.gff
