├── .gitignore ├── .vscode └── settings.json ├── LICENSE ├── README.md ├── compare_genomes.yml ├── config ├── comparisons_4DTv.txt ├── dates.txt ├── genes.txt ├── params.config ├── process.config ├── urls.txt └── venn_species_max_5.txt ├── misc ├── KaKs_ratio_plots │ ├── GSTU13-OG0000041.aln-1.pw.kaks.svg │ ├── GSTU13-OG0000041.aln-2.pw.kaks.svg │ ├── GSTU13-OG0000041.aln-4.pw.kaks.svg │ ├── GSTU13-OG0000041.aln-5.pw.kaks.svg │ ├── GSTU13-OG0000041.aln-7.pw.kaks.svg │ ├── GSTU13-OG0000394.aln-1.pw.kaks.svg │ ├── GSTU13-OG0000394.aln-2.pw.kaks.svg │ ├── GSTU13-OG0001872.aln-1.pw.kaks.svg │ ├── GSTU13-OG0003331.aln-1.pw.kaks.svg │ ├── GSTU13-OG0006358.aln-1.pw.kaks.svg │ └── GSTU13-OG0006358.aln-2.pw.kaks.svg └── compare_genomes_workflow.svg ├── modules ├── GO_enrichment.nf ├── assess_WGD.nf ├── assess_specific_genes.nf ├── gene_family_contraction_expansion.nf ├── misc │ ├── installation_from_scratch.md │ └── test.nf ├── orthofinder.nf ├── plot_tree_conex_venn_4DTv.nf ├── setup.nf ├── single_gene_orthogroups_4DTv.nf └── single_gene_orthogroups_tree.nf ├── run.sh └── scripts ├── calculate_4DTv.jl ├── count_genes_per_ortholog_paralog_classes.jl ├── extract_multi_gene_orthogroups.sh ├── extract_sequence_using_name_query.jl ├── extract_single_gene_orthogroups.jl ├── orthogroup_classification_gene_family_GO_terms.jl ├── plot_KaKs_across_windows.R ├── plot_tree_singleGeneConex_venn_4DTv.R ├── reformat_fasta_sequence.jl ├── split_alignment_pairs.jl └── test.sh /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffersonfparil/compare_genomes/HEAD/.gitignore -------------------------------------------------------------------------------- /.vscode/settings.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffersonfparil/compare_genomes/HEAD/.vscode/settings.json 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