├── .gitignore ├── LICENSE ├── PanPA ├── Alignment.pxd ├── Alignment.pyx ├── Graph.pxd ├── Graph.pyx ├── Node.pxd ├── Node.pyx ├── __init__.py ├── _main.pyx ├── alignment_test.pyx ├── constants.py ├── debugging_functions.py ├── find_seeds.py ├── fm_index_from_msa.py ├── graph_edit_distance.pxd ├── graph_edit_distance.pyx ├── graph_from_msa.pyx ├── graph_io.py ├── graph_smith_waterman.pxd ├── graph_smith_waterman.pyx ├── graph_smith_waterman_frameshift_aware.pxd ├── graph_smith_waterman_frameshift_aware.pyx ├── graph_test.pyx ├── index_sequences.pyx ├── main.py ├── node_test.pyx ├── read_fasta.py ├── reverse_complement_fast.pyx ├── running_test.pyx ├── smith_waterman.pyx ├── test_Alignment.py ├── test_Graph.py ├── test_Node.py ├── test_frameshift_alignment.py ├── translate_read.pyx ├── turn_sub_matrix_to_vector.py └── version.py ├── README.md ├── accessions ├── README.md └── accession_numbers_of_samples.xlsx ├── environment.yml ├── old_pyproject.toml ├── requirements.txt ├── scripts ├── alignment_validation │ ├── clusters_stats.py │ ├── extract_random_sequences.py │ ├── get_matches_mismatches.py │ ├── move_1seq_file_to_msa.py │ ├── panpa_alignments_stats.py │ └── validate_match_miss.py ├── big_table_to_tsv.py ├── big_table_upset_plot.py ├── build_reads_table.py ├── download_assemblies_ncbi.py ├── extract_clusters.py ├── extract_patric_protein.py ├── extract_seqs_from_ref.py ├── fasta_fastq_statistics.sh ├── fasta_to_upper.py ├── filter_gaf_alignment_id.sh ├── filter_gaf_alignment_length_percentage.sh ├── filter_sam_alignment_id.py ├── filter_sam_alignment_size.py ├── frameshift_aware_alignment.py ├── get_order_from_gaf.py ├── msa_checker.py ├── run_clustalo.py ├── running_mafft.smk ├── salmonella_experiment_stats.sh ├── sam_stats.py ├── separate_proteins.py ├── separate_seqs_from_fasta.py └── separate_sequences_big_table.py ├── setup.py └── tutorial ├── README.md ├── download_proteins.sh └── ftp_links.txt /.gitignore: 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