├── .coveragerc ├── .gitattributes ├── .github └── workflows │ └── ci.yml ├── .gitignore ├── .pylintrc ├── CITATION.bib ├── CITATION.cff ├── Dockerfile ├── LICENSE ├── README.md ├── appveyor.yml ├── docker_banner.sh ├── docs ├── Makefile ├── make.bat └── source │ ├── _static │ └── docker.gif │ ├── conf.py │ ├── index.rst │ ├── installation.rst │ ├── introduction.rst │ ├── output.rst │ └── programs │ ├── add_transcripts.rst │ ├── programs.rst │ ├── thoraxe.rst │ └── transcript_query.rst ├── requirements.txt ├── setup.cfg ├── setup.py ├── tests ├── data │ ├── CAMK2A │ │ └── Ensembl │ │ │ ├── exonstable.tsv │ │ │ ├── sequences.fasta │ │ │ ├── tree.nh │ │ │ └── tsl.csv │ ├── GPRIN1 │ │ └── Ensembl │ │ │ ├── exonstable.tsv │ │ │ ├── sequences.fasta │ │ │ ├── tree.nh │ │ │ └── tsl.csv │ ├── KIF1B │ │ └── Ensembl │ │ │ ├── ensembl_version.csv │ │ │ ├── exonstable.tsv │ │ │ ├── sequences.fasta │ │ │ ├── tree.nh │ │ │ └── tsl.csv │ ├── MAPK8 │ │ └── Ensembl │ │ │ ├── exonstable.tsv │ │ │ ├── sequences.fasta │ │ │ ├── tree.nh │ │ │ └── tsl.csv │ ├── MAPK8_all │ │ └── Ensembl │ │ │ ├── ensembl_version.csv │ │ │ ├── exonstable.tsv │ │ │ ├── sequences.fasta │ │ │ ├── tree.nh │ │ │ └── tsl.csv │ ├── MAPK8_output │ │ └── thoraxe │ │ │ ├── _intermediate │ │ │ ├── chimeric_alignment_1.fasta │ │ │ ├── chimeric_alignment_10.fasta │ │ │ ├── chimeric_alignment_11.fasta │ │ │ ├── chimeric_alignment_12.fasta │ │ │ ├── chimeric_alignment_13.fasta │ │ │ ├── chimeric_alignment_14.fasta │ │ │ ├── chimeric_alignment_15.fasta │ │ │ ├── chimeric_alignment_16.fasta │ │ │ ├── chimeric_alignment_17.fasta │ │ │ ├── chimeric_alignment_18.fasta │ │ │ ├── chimeric_alignment_19.fasta │ │ │ ├── chimeric_alignment_2.fasta │ │ │ ├── chimeric_alignment_21.fasta │ │ │ ├── chimeric_alignment_22.fasta │ │ │ ├── chimeric_alignment_3.fasta │ │ │ ├── chimeric_alignment_4.fasta │ │ │ ├── chimeric_alignment_5.fasta │ │ │ ├── chimeric_alignment_6.fasta │ │ │ ├── chimeric_alignment_7.fasta │ │ │ ├── chimeric_alignment_8.fasta │ │ │ ├── chimeric_alignment_9.fasta │ │ │ ├── gene_ids_1.txt │ │ │ ├── gene_ids_10.txt │ │ │ ├── gene_ids_11.txt │ │ │ ├── gene_ids_12.txt │ │ │ ├── gene_ids_13.txt │ │ │ ├── gene_ids_14.txt │ │ │ ├── gene_ids_15.txt │ │ │ ├── gene_ids_16.txt │ │ │ ├── gene_ids_17.txt │ │ │ ├── gene_ids_18.txt │ │ │ ├── gene_ids_19.txt │ │ │ ├── gene_ids_2.txt │ │ │ ├── gene_ids_21.txt │ │ │ ├── gene_ids_22.txt │ │ │ ├── gene_ids_3.txt │ │ │ ├── gene_ids_4.txt │ │ │ ├── gene_ids_5.txt │ │ │ ├── gene_ids_6.txt │ │ │ ├── gene_ids_7.txt │ │ │ ├── gene_ids_8.txt │ │ │ ├── gene_ids_9.txt │ │ │ ├── msa_matrix_1.txt │ │ │ ├── msa_matrix_10.txt │ │ │ ├── msa_matrix_11.txt │ │ │ ├── msa_matrix_12.txt │ │ │ ├── msa_matrix_13.txt │ │ │ ├── msa_matrix_14.txt │ │ │ ├── msa_matrix_15.txt │ │ │ ├── msa_matrix_16.txt │ │ │ ├── msa_matrix_17.txt │ │ │ ├── msa_matrix_18.txt │ │ │ ├── msa_matrix_19.txt │ │ │ ├── msa_matrix_2.txt │ │ │ ├── msa_matrix_21.txt │ │ │ ├── msa_matrix_22.txt │ │ │ ├── msa_matrix_3.txt │ │ │ ├── msa_matrix_4.txt │ │ │ ├── msa_matrix_5.txt │ │ │ ├── msa_matrix_6.txt │ │ │ ├── msa_matrix_7.txt │ │ │ ├── msa_matrix_8.txt │ │ │ ├── msa_matrix_9.txt │ │ │ ├── subexon_table.csv │ │ │ ├── subexon_table_1.csv │ │ │ ├── subexon_table_10.csv │ │ │ ├── subexon_table_11.csv │ │ │ ├── subexon_table_12.csv │ │ │ ├── subexon_table_13.csv │ │ │ ├── subexon_table_14.csv │ │ │ ├── subexon_table_15.csv │ │ │ ├── subexon_table_16.csv │ │ │ ├── subexon_table_17.csv │ │ │ ├── subexon_table_18.csv │ │ │ ├── subexon_table_19.csv │ │ │ ├── subexon_table_2.csv │ │ │ ├── subexon_table_21.csv │ │ │ ├── subexon_table_22.csv │ │ │ ├── subexon_table_3.csv │ │ │ ├── subexon_table_4.csv │ │ │ ├── subexon_table_5.csv │ │ │ ├── subexon_table_6.csv │ │ │ ├── subexon_table_7.csv │ │ │ ├── subexon_table_8.csv │ │ │ ├── subexon_table_9.csv │ │ │ └── transcript_table.csv │ │ │ ├── ases_table.csv │ │ │ ├── msa │ │ │ ├── msa_s_exon_10_0.fasta │ │ │ ├── msa_s_exon_11_0.fasta │ │ │ ├── msa_s_exon_11_1.fasta │ │ │ ├── msa_s_exon_12_0.fasta │ │ │ ├── msa_s_exon_13_0.fasta │ │ │ ├── msa_s_exon_14_0.fasta │ │ │ ├── msa_s_exon_15_0.fasta │ │ │ ├── msa_s_exon_16_0.fasta │ │ │ ├── msa_s_exon_17_0.fasta │ │ │ ├── msa_s_exon_18_0.fasta │ │ │ ├── msa_s_exon_19_0.fasta │ │ │ ├── msa_s_exon_1_0.fasta │ │ │ ├── msa_s_exon_1_1.fasta │ │ │ ├── msa_s_exon_21_0.fasta │ │ │ ├── msa_s_exon_21_1.fasta │ │ │ ├── msa_s_exon_22_0.fasta │ │ │ ├── msa_s_exon_2_0.fasta │ │ │ ├── msa_s_exon_2_1.fasta │ │ │ ├── msa_s_exon_3_0.fasta │ │ │ ├── msa_s_exon_3_1.fasta │ │ │ ├── msa_s_exon_4_0.fasta │ │ │ ├── msa_s_exon_4_1.fasta │ │ │ ├── msa_s_exon_5_0.fasta │ │ │ ├── msa_s_exon_6_0.fasta │ │ │ ├── msa_s_exon_6_1.fasta │ │ │ ├── msa_s_exon_6_2.fasta │ │ │ ├── msa_s_exon_7_0.fasta │ │ │ ├── msa_s_exon_7_1.fasta │ │ │ ├── msa_s_exon_7_2.fasta │ │ │ ├── msa_s_exon_7_3.fasta │ │ │ ├── msa_s_exon_8_0.fasta │ │ │ └── msa_s_exon_9_0.fasta │ │ │ ├── path_table.csv │ │ │ ├── phylosofs │ │ │ ├── s_exons.tsv │ │ │ ├── transcripts.pir │ │ │ ├── transcripts.txt │ │ │ └── tree.nh │ │ │ ├── s_exon_table.csv │ │ │ └── splice_graph.gml │ ├── POLR3B │ │ └── Ensembl │ │ │ ├── ensembl_version.csv │ │ │ ├── exonstable.tsv │ │ │ ├── sequences.fasta │ │ │ ├── tree.nh │ │ │ └── tsl.csv │ ├── POLR3B_output │ │ └── thoraxe │ │ │ ├── _intermediate │ │ │ ├── chimeric_alignment_1.fasta │ │ │ ├── chimeric_alignment_10.fasta │ │ │ ├── chimeric_alignment_11.fasta │ │ │ ├── chimeric_alignment_12.fasta │ │ │ ├── chimeric_alignment_13.fasta │ │ │ ├── chimeric_alignment_14.fasta │ │ │ ├── chimeric_alignment_15.fasta │ │ │ ├── chimeric_alignment_16.fasta │ │ │ ├── chimeric_alignment_17.fasta │ │ │ ├── chimeric_alignment_18.fasta │ │ │ ├── chimeric_alignment_19.fasta │ │ │ ├── chimeric_alignment_2.fasta │ │ │ ├── chimeric_alignment_20.fasta │ │ │ ├── chimeric_alignment_21.fasta │ │ │ ├── chimeric_alignment_22.fasta │ │ │ ├── chimeric_alignment_23.fasta │ │ │ ├── chimeric_alignment_24.fasta │ │ │ ├── chimeric_alignment_25.fasta │ │ │ ├── chimeric_alignment_26.fasta │ │ │ ├── chimeric_alignment_27.fasta │ │ │ ├── chimeric_alignment_28.fasta │ │ │ ├── chimeric_alignment_29.fasta │ │ │ ├── chimeric_alignment_3.fasta │ │ │ ├── chimeric_alignment_30.fasta │ │ │ ├── chimeric_alignment_31.fasta │ │ │ ├── chimeric_alignment_32.fasta │ │ │ ├── chimeric_alignment_33.fasta │ │ │ ├── chimeric_alignment_34.fasta │ │ │ ├── chimeric_alignment_35.fasta │ │ │ ├── chimeric_alignment_36.fasta │ │ │ ├── chimeric_alignment_37.fasta │ │ │ ├── chimeric_alignment_38.fasta │ │ │ ├── chimeric_alignment_39.fasta │ │ │ ├── chimeric_alignment_4.fasta │ │ │ ├── chimeric_alignment_40.fasta │ │ │ ├── chimeric_alignment_41.fasta │ │ │ ├── chimeric_alignment_42.fasta │ │ │ ├── chimeric_alignment_43.fasta │ │ │ ├── chimeric_alignment_44.fasta │ │ │ ├── chimeric_alignment_45.fasta │ │ │ ├── chimeric_alignment_46.fasta │ │ │ ├── chimeric_alignment_47.fasta │ │ │ ├── chimeric_alignment_48.fasta │ │ │ ├── chimeric_alignment_49.fasta │ │ │ ├── chimeric_alignment_5.fasta │ │ │ ├── chimeric_alignment_50.fasta │ │ │ ├── chimeric_alignment_51.fasta │ │ │ ├── chimeric_alignment_53.fasta │ │ │ ├── chimeric_alignment_54.fasta │ │ │ ├── chimeric_alignment_55.fasta │ │ │ ├── chimeric_alignment_57.fasta │ │ │ ├── chimeric_alignment_6.fasta │ │ │ ├── chimeric_alignment_7.fasta │ │ │ ├── chimeric_alignment_8.fasta │ │ │ ├── chimeric_alignment_9.fasta │ │ │ ├── gene_ids_1.txt │ │ │ ├── gene_ids_10.txt │ │ │ ├── gene_ids_11.txt │ │ │ ├── gene_ids_12.txt │ │ │ ├── gene_ids_13.txt │ │ │ ├── gene_ids_14.txt │ │ │ ├── gene_ids_15.txt │ │ │ ├── gene_ids_16.txt │ │ │ ├── gene_ids_17.txt │ │ │ ├── gene_ids_18.txt │ │ │ ├── gene_ids_19.txt │ │ │ ├── gene_ids_2.txt │ │ │ ├── gene_ids_20.txt │ │ │ ├── gene_ids_21.txt │ │ │ ├── gene_ids_22.txt │ │ │ ├── gene_ids_23.txt │ │ │ ├── gene_ids_24.txt │ │ │ ├── gene_ids_25.txt │ │ │ ├── gene_ids_26.txt │ │ │ ├── gene_ids_27.txt │ │ │ ├── gene_ids_28.txt │ │ │ ├── gene_ids_29.txt │ │ │ ├── gene_ids_3.txt │ │ │ ├── gene_ids_30.txt │ │ │ ├── gene_ids_31.txt │ │ │ ├── gene_ids_32.txt │ │ │ ├── gene_ids_33.txt │ │ │ ├── gene_ids_34.txt │ │ │ ├── gene_ids_35.txt │ │ │ ├── gene_ids_36.txt │ │ │ ├── gene_ids_37.txt │ │ │ ├── gene_ids_38.txt │ │ │ ├── gene_ids_39.txt │ │ │ ├── gene_ids_4.txt │ │ │ ├── gene_ids_40.txt │ │ │ ├── gene_ids_41.txt │ │ │ ├── gene_ids_42.txt │ │ │ ├── gene_ids_43.txt │ │ │ ├── gene_ids_44.txt │ │ │ ├── gene_ids_45.txt │ │ │ ├── gene_ids_46.txt │ │ │ ├── gene_ids_47.txt │ │ │ ├── gene_ids_48.txt │ │ │ ├── gene_ids_49.txt │ │ │ ├── gene_ids_5.txt │ │ │ ├── gene_ids_50.txt │ │ │ ├── gene_ids_51.txt │ │ │ ├── gene_ids_53.txt │ │ │ ├── gene_ids_54.txt │ │ │ ├── gene_ids_55.txt │ │ │ ├── gene_ids_57.txt │ │ │ ├── gene_ids_6.txt │ │ │ ├── gene_ids_7.txt │ │ │ ├── gene_ids_8.txt │ │ │ ├── gene_ids_9.txt │ │ │ ├── msa_matrix_1.txt │ │ │ ├── msa_matrix_10.txt │ │ │ ├── msa_matrix_11.txt │ │ │ ├── msa_matrix_12.txt │ │ │ ├── msa_matrix_13.txt │ │ │ ├── msa_matrix_14.txt │ │ │ ├── msa_matrix_15.txt │ │ │ ├── msa_matrix_16.txt │ │ │ ├── msa_matrix_17.txt │ │ │ ├── msa_matrix_18.txt │ │ │ ├── msa_matrix_19.txt │ │ │ ├── msa_matrix_2.txt │ │ │ ├── msa_matrix_20.txt │ │ │ ├── msa_matrix_21.txt │ │ │ ├── msa_matrix_22.txt │ │ │ ├── msa_matrix_23.txt │ │ │ ├── msa_matrix_24.txt │ │ │ ├── msa_matrix_25.txt │ │ │ ├── msa_matrix_26.txt │ │ │ ├── msa_matrix_27.txt │ │ │ ├── msa_matrix_28.txt │ │ │ ├── msa_matrix_29.txt │ │ │ ├── msa_matrix_3.txt │ │ │ ├── msa_matrix_30.txt │ │ │ ├── msa_matrix_31.txt │ │ │ ├── msa_matrix_32.txt │ │ │ ├── msa_matrix_33.txt │ │ │ ├── msa_matrix_34.txt │ │ │ ├── msa_matrix_35.txt │ │ │ ├── msa_matrix_36.txt │ │ │ ├── msa_matrix_37.txt │ │ │ ├── msa_matrix_38.txt │ │ │ ├── msa_matrix_39.txt │ │ │ ├── msa_matrix_4.txt │ │ │ ├── msa_matrix_40.txt │ │ │ ├── msa_matrix_41.txt │ │ │ ├── msa_matrix_42.txt │ │ │ ├── msa_matrix_43.txt │ │ │ ├── msa_matrix_44.txt │ │ │ ├── msa_matrix_45.txt │ │ │ ├── msa_matrix_46.txt │ │ │ ├── msa_matrix_47.txt │ │ │ ├── msa_matrix_48.txt │ │ │ ├── msa_matrix_49.txt │ │ │ ├── msa_matrix_5.txt │ │ │ ├── msa_matrix_50.txt │ │ │ ├── msa_matrix_51.txt │ │ │ ├── msa_matrix_53.txt │ │ │ ├── msa_matrix_54.txt │ │ │ ├── msa_matrix_55.txt │ │ │ ├── msa_matrix_57.txt │ │ │ ├── msa_matrix_6.txt │ │ │ ├── msa_matrix_7.txt │ │ │ ├── msa_matrix_8.txt │ │ │ ├── msa_matrix_9.txt │ │ │ ├── subexon_table.csv │ │ │ ├── subexon_table_1.csv │ │ │ ├── subexon_table_10.csv │ │ │ ├── subexon_table_11.csv │ │ │ ├── subexon_table_12.csv │ │ │ ├── subexon_table_13.csv │ │ │ ├── subexon_table_14.csv │ │ │ ├── subexon_table_15.csv │ │ │ ├── subexon_table_16.csv │ │ │ ├── subexon_table_17.csv │ │ │ ├── subexon_table_18.csv │ │ │ ├── subexon_table_19.csv │ │ │ ├── subexon_table_2.csv │ │ │ ├── subexon_table_20.csv │ │ │ ├── subexon_table_21.csv │ │ │ ├── subexon_table_22.csv │ │ │ ├── subexon_table_23.csv │ │ │ ├── subexon_table_24.csv │ │ │ ├── subexon_table_25.csv │ │ │ ├── subexon_table_26.csv │ │ │ ├── subexon_table_27.csv │ │ │ ├── subexon_table_28.csv │ │ │ ├── subexon_table_29.csv │ │ │ ├── subexon_table_3.csv │ │ │ ├── subexon_table_30.csv │ │ │ ├── subexon_table_31.csv │ │ │ ├── subexon_table_32.csv │ │ │ ├── subexon_table_33.csv │ │ │ ├── subexon_table_34.csv │ │ │ ├── subexon_table_35.csv │ │ │ ├── subexon_table_36.csv │ │ │ ├── subexon_table_37.csv │ │ │ ├── subexon_table_38.csv │ │ │ ├── subexon_table_39.csv │ │ │ ├── subexon_table_4.csv │ │ │ ├── subexon_table_40.csv │ │ │ ├── subexon_table_41.csv │ │ │ ├── subexon_table_42.csv │ │ │ ├── subexon_table_43.csv │ │ │ ├── subexon_table_44.csv │ │ │ ├── subexon_table_45.csv │ │ │ ├── subexon_table_46.csv │ │ │ ├── subexon_table_47.csv │ │ │ ├── subexon_table_48.csv │ │ │ ├── subexon_table_49.csv │ │ │ ├── subexon_table_5.csv │ │ │ ├── subexon_table_50.csv │ │ │ ├── subexon_table_51.csv │ │ │ ├── subexon_table_53.csv │ │ │ ├── subexon_table_54.csv │ │ │ ├── subexon_table_55.csv │ │ │ ├── subexon_table_57.csv │ │ │ ├── subexon_table_6.csv │ │ │ ├── subexon_table_7.csv │ │ │ ├── subexon_table_8.csv │ │ │ ├── subexon_table_9.csv │ │ │ └── transcript_table.csv │ │ │ ├── ases_table.csv │ │ │ ├── msa │ │ │ ├── msa_s_exon_10_0.fasta │ │ │ ├── msa_s_exon_11_0.fasta │ │ │ ├── msa_s_exon_12_0.fasta │ │ │ ├── msa_s_exon_12_1.fasta │ │ │ ├── msa_s_exon_13_0.fasta │ │ │ ├── msa_s_exon_14_0.fasta │ │ │ ├── msa_s_exon_15_0.fasta │ │ │ ├── msa_s_exon_16_0.fasta │ │ │ ├── msa_s_exon_17_0.fasta │ │ │ ├── msa_s_exon_17_1.fasta │ │ │ ├── msa_s_exon_18_0.fasta │ │ │ ├── msa_s_exon_19_0.fasta │ │ │ ├── msa_s_exon_1_0.fasta │ │ │ ├── msa_s_exon_20_0.fasta │ │ │ ├── msa_s_exon_21_0.fasta │ │ │ ├── msa_s_exon_22_0.fasta │ │ │ ├── msa_s_exon_23_0.fasta │ │ │ ├── msa_s_exon_24_0.fasta │ │ │ ├── msa_s_exon_25_0.fasta │ │ │ ├── msa_s_exon_25_1.fasta │ │ │ ├── msa_s_exon_25_2.fasta │ │ │ ├── msa_s_exon_26_0.fasta │ │ │ ├── msa_s_exon_27_0.fasta │ │ │ ├── msa_s_exon_27_1.fasta │ │ │ ├── msa_s_exon_28_0.fasta │ │ │ ├── msa_s_exon_29_0.fasta │ │ │ ├── msa_s_exon_2_0.fasta │ │ │ ├── msa_s_exon_30_0.fasta │ │ │ ├── msa_s_exon_31_0.fasta │ │ │ ├── msa_s_exon_32_0.fasta │ │ │ ├── msa_s_exon_33_0.fasta │ │ │ ├── msa_s_exon_34_0.fasta │ │ │ ├── msa_s_exon_35_0.fasta │ │ │ ├── msa_s_exon_36_0.fasta │ │ │ ├── msa_s_exon_37_0.fasta │ │ │ ├── msa_s_exon_38_0.fasta │ │ │ ├── msa_s_exon_39_0.fasta │ │ │ ├── msa_s_exon_3_0.fasta │ │ │ ├── msa_s_exon_40_0.fasta │ │ │ ├── msa_s_exon_41_0.fasta │ │ │ ├── msa_s_exon_42_0.fasta │ │ │ ├── msa_s_exon_43_0.fasta │ │ │ ├── msa_s_exon_44_0.fasta │ │ │ ├── msa_s_exon_45_0.fasta │ │ │ ├── msa_s_exon_46_0.fasta │ │ │ ├── msa_s_exon_47_0.fasta │ │ │ ├── msa_s_exon_48_0.fasta │ │ │ ├── msa_s_exon_48_1.fasta │ │ │ ├── msa_s_exon_49_0.fasta │ │ │ ├── msa_s_exon_4_0.fasta │ │ │ ├── msa_s_exon_50_0.fasta │ │ │ ├── msa_s_exon_51_0.fasta │ │ │ ├── msa_s_exon_53_0.fasta │ │ │ ├── msa_s_exon_54_0.fasta │ │ │ ├── msa_s_exon_55_0.fasta │ │ │ ├── msa_s_exon_57_0.fasta │ │ │ ├── msa_s_exon_5_0.fasta │ │ │ ├── msa_s_exon_6_0.fasta │ │ │ ├── msa_s_exon_7_0.fasta │ │ │ ├── msa_s_exon_7_1.fasta │ │ │ ├── msa_s_exon_7_2.fasta │ │ │ ├── msa_s_exon_7_3.fasta │ │ │ ├── msa_s_exon_8_0.fasta │ │ │ └── msa_s_exon_9_0.fasta │ │ │ ├── path_table.csv │ │ │ ├── phylosofs │ │ │ ├── s_exons.tsv │ │ │ ├── transcripts.pir │ │ │ ├── transcripts.txt │ │ │ └── tree.nh │ │ │ ├── s_exon_table.csv │ │ │ └── splice_graph.gml │ ├── species_list.txt │ ├── update_outputs.sh │ └── user_transcript.csv ├── test_add_transcripts.py ├── test_alignment.py ├── test_ases.py ├── test_merging.py ├── test_pir.py ├── test_s_exon_ordering.py ├── test_subexons.py ├── test_thoraxe.py ├── test_transcript_info.py └── test_transcript_query.py └── thoraxe ├── __init__.py ├── add_transcripts ├── __init__.py └── add_transcripts.py ├── subexons ├── __init__.py ├── alignment.py ├── ases.py ├── assets │ └── cluster_plots.html ├── graph.py ├── phylosofs.py ├── plot.py ├── rescue.py ├── subexons.py └── tidy.py ├── thoraxe.py ├── transcript_info ├── __init__.py ├── clusters.py ├── exon_clustering.py ├── phases.py └── transcript_info.py ├── transcript_query ├── __init__.py └── transcript_query.py ├── utils ├── __init__.py ├── folders.py ├── species.py ├── split.py └── windows.py └── version.py /.coveragerc: -------------------------------------------------------------------------------- 1 | [run] 2 | source=exonhomology 3 | -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PhyloSofS-Team/thoraxe/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/workflows/ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PhyloSofS-Team/thoraxe/HEAD/.github/workflows/ci.yml 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