├── .infos ├── input_data_info.md ├── install.md └── r_env.yml ├── .pictures ├── Fig1.png ├── Fig10.png ├── Fig2.png ├── Fig3.png ├── Fig4.png ├── Fig5.png ├── Fig6.A.png ├── Fig6.B.svg ├── Fig7.svg ├── Fig8.png ├── Fig9.png ├── Figure11.svg ├── Figure12.svg ├── depth.png └── pdf │ ├── Ds_and_arrangements.pdf │ ├── ancestral_sphap1.pdf │ ├── dotplot_prim_ali_bwaln.hap1_hap2.paf.pdf │ ├── hap1hap2.svg │ ├── subset_geneOrder_useRegionF.pdf │ └── synteny_aln.hap1_hap2.paf_hap1_A1_hap2_A2.pdf ├── 00_scripts ├── 00_rename.fasta.sh ├── 00_rename_fasta.py ├── 01_trimmomatic_PE.sh ├── 01_trimmomatic_SE.sh ├── 02_gmap.sh ├── 03_gsnap_PE.sh ├── 03_gsnap_PE_array.sh ├── 03_gsnap_SE.sh ├── 04_count_mapped_read.sh ├── 04_count_mapped_read_SE.sh ├── 05_repeatmodeler.sh ├── 06_braker.sh ├── 06_braker_db_array.sh ├── 06_braker_rnaseq.sh ├── 07_busco_after_braker.sh ├── 08_braker_reshaping.sh ├── 09_tsebra.sh ├── 10_diamond_blast.sh ├── 11_run_GeneSpace_and_firstplots.sh ├── 11_run_GeneSpace_paml_ideogram.sh ├── 12_command_line.paml.sh ├── 12_paml_parallel_version.sh ├── Rscripts │ ├── 01.run_geneSpace.R │ ├── 02.plot_geneSpace.R │ ├── 03.plot_paml.R │ ├── 04.ideogram.R │ ├── 05_plot_circos.R │ ├── 06.MCP_model_comp.R │ ├── dotplot_paf.R │ ├── plot_dp.R │ ├── plot_mapq.R │ └── synteny_plot.R ├── after_braker │ ├── 00_extract_braker_best_run.sh │ ├── 01_remove_dup_and_simplify.gtf.sh │ ├── 03_minprot2.sh │ ├── bedtools_check.Sh │ ├── deprecated │ │ ├── 01_remove_redundant_genemark.sh │ │ ├── 02_simplify_gtf.sh │ │ └── 04_rm_dup.sh │ └── rename.fasta_ids.sh ├── deprecated │ ├── 01.plot_paml.R │ ├── 01_trimmomatic.sh │ ├── 05_merge.filter.sort.sh │ ├── 07_busco_after_braker.sh │ ├── 08_tsebra_3dataset.sh │ ├── 09_extractcds.sh │ └── 10.keep.longest_transcript_from_DB.sh ├── extract_singlecopy.sh ├── get_interpro.sh ├── get_uniprot.sh ├── launch_rnaseq.sh ├── launch_step05_to_08.sh ├── launch_trimm.sh ├── long_reads │ ├── isoseqv2_minimap_asm20.sh │ ├── isoseqv2_minimap_target_species.sh │ └── pbmm_and_isoseq3.sh ├── quality.check.sh ├── sedme.sh ├── slurm_code │ ├── 01_submit_trimmomatic.sh │ ├── 02_submit_gmap.sh │ ├── 03_gsnap_array.sh │ ├── 03_submit_gsnap.sh │ ├── 03_submit_gsnap_array.sh │ ├── 04_submit_repeatmodeler.sh │ ├── 05_braker_RNAseq.sh │ ├── 05_braker_db_array.sh │ ├── 05_prepare_data_braker.sh │ ├── 05_submit_braker.sh │ ├── 06_reshape_braker_output.sh │ ├── 07_dataprep_opt3_opt4_opt5.sh │ ├── 08_submit_genespace_and_first_plot_only.sh │ ├── 08_submit_genespace_paml_and_plot.sh │ ├── 09_paml_preparation_slurm.sh │ ├── 10_submit_paml_parallel.sh │ ├── 11_changepoint_only.sh │ ├── 12_ideogram_and_circos_after_changepoint.sh │ └── runall_slurm_workflow.sh └── utility_scripts │ ├── 01.recode_braker_output.py │ ├── 02.Make_synteny_table.py │ ├── Fix_Augustus_gtf.pl │ ├── awk_fasta_length.sh │ ├── awk_linearize_fasta.sh │ ├── awk_total_length.txt │ ├── busco.sh │ ├── count_read_fastq.sh │ ├── fa2prot.sh │ ├── generateReport.py │ ├── predictionAnalysis.py │ ├── printLongestIsoforms.py │ ├── rename_and_convert_gtf.sh │ ├── split.fasta.sh │ └── split.gff.sh ├── INSTALL ├── INSTALL.md ├── annotation_env.yml ├── busco_env.yml ├── check_deps.sh ├── dependencies.sh ├── repeatmodeler.yml └── translatorx_vLocal.pl ├── LICENSE ├── README.md ├── config ├── codeml.ctl ├── colors ├── config ├── cpu_mem ├── default.cfg ├── details_on_config.md ├── list_of_dependencies.txt └── yn00_template.ctl ├── example_data ├── .pictures │ ├── Fig1.stickleback.png │ ├── Fig2.stickleback.png │ ├── Fig3.stickleback.png │ ├── Fig4.stickleback.png │ ├── Fig5.stickleback.svg │ ├── Fig6.stickleback.svg │ └── FigS30_test.png ├── MCP_with_priors_example6.R ├── Mlag129.centromere.bed ├── Mlag129A1.TE.bed ├── Mlag129A1.fa.gz ├── Mlag129A1.gff.gz ├── Mlag129A1.gtf.gz ├── TE.fa.gz ├── chromosomes.txt ├── config7.md ├── example.config ├── example1.config ├── example1.md ├── example2.config ├── example2.md ├── example3.config ├── example3.md ├── example3figure │ ├── Fig1.png │ ├── Fig1.svg │ ├── Fig10.svg │ ├── Fig2.png │ ├── Fig2.svg │ ├── Fig3.png │ ├── Fig3b.png │ ├── Fig3b.svg │ ├── Fig4.svg │ ├── Fig5.svg │ ├── Fig6.svg │ ├── Fig7.svg │ ├── Fig8.svg │ ├── Fig9.svg │ ├── dS.values.forchangepoint.txt │ ├── joint_genome1.hap1_genome2.hap2.bed │ ├── model_weights.txt │ ├── results_YN.txt │ └── single.copy.orthologs ├── example4.config ├── example4.md ├── example5.config ├── example5.md ├── example5data │ └── readme.md ├── example6.config ├── example6.md ├── example7.md ├── example8.config ├── example8.md ├── example9.config ├── example9.md ├── example9figure │ ├── 0.synteny.svg │ ├── 1.circos.svg │ ├── 3.ideogram.svg │ └── 4.dS.svg ├── genome1.fa.gz ├── genome2.fa.gz ├── rnaseq.list.example5.txt ├── rnaseq.list.txt ├── scaffold.txt ├── scaffold_example3.txt └── scaffold_example5.txt ├── haplo1 ├── 01_raw │ └── Readme ├── 02_trimmed │ └── .gitignore └── 03_genome │ └── Readme ├── haplo2 ├── 01_raw │ └── Readme 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