├── .gitignore ├── LICENSE ├── README.md ├── bin ├── FFProblem.py ├── GSGraph.py ├── ILPBuilder.py ├── combine_roary_ilp.py ├── concat_coreMSA.py ├── cplexsol_to_simple.py ├── create_msa_tree.py ├── derive_ilp_solutions.py ├── generate_html.py ├── helper │ └── rearrange │ │ ├── config.py │ │ ├── findPOI.py │ │ ├── main.py │ │ └── rearranging.py ├── mmseq2tsv.py └── rename.sh ├── configs ├── conda.config ├── container.config ├── local.config └── nodes.config ├── data ├── Cav_10DC88.fasta ├── Cav_11DC096.fasta ├── Cga_08-1274-3.fasta ├── Cga_12-4358.fasta ├── Ctr_A-HAR-13.fasta ├── example-results │ ├── README.md │ ├── core_genome-modeltest.treefile │ ├── core_genome-modeltest.treefile.png │ ├── html-report │ │ ├── images │ │ │ ├── details_close.png │ │ │ ├── details_open.png │ │ │ ├── sort_asc.png │ │ │ ├── sort_asc_disabled.png │ │ │ ├── sort_both.png │ │ │ ├── sort_desc.png │ │ │ └── sort_desc_disabled.png │ │ ├── jquery-3.3.1.min.js │ │ ├── jquery.dataTables.min.css │ │ ├── jquery.dataTables.min.js │ │ ├── objects.txt │ │ ├── ribap-report.png │ │ └── ribap.html │ ├── upsetr.png │ └── upsetr.svg └── web.tar.gz ├── envs ├── basics.yaml ├── bioruby.yaml ├── cdhit.yaml ├── fasttree.yaml ├── iqtree.yaml ├── mafft.yaml ├── mmseqs2.yaml ├── newick_utils.yaml ├── prokka.yaml ├── python_ribap.yaml ├── raxml.yaml ├── roary.yaml └── upsetr.yaml ├── figures ├── dag.png ├── riba.pdf ├── riba.svg ├── ribap-overview.png └── ribap.gif ├── legacy ├── ILP.py ├── INSTALL.sh ├── combine_msa.nf ├── glpk.yaml ├── ilp_solve.nf ├── mmseqs2tsv.nf ├── raxml.nf └── ribap.sh ├── modules ├── combine_roary_ilp.nf ├── fasttree.nf ├── filter_alignment.nf ├── generate_html.nf ├── generate_upsetr_input.nf ├── ilp_refinement.nf ├── iqtree.nf ├── mafft.nf ├── mmseqs2.nf ├── nexus_core.nf ├── nw_display.nf ├── prepare_msa.nf ├── prokka.nf ├── rename.nf ├── roary.nf ├── strain_ids.nf └── upsetr.nf ├── nextflow.config ├── ribap.nf └── web ├── images ├── details_close.png ├── details_open.png 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