├── LICENSE ├── README.md ├── bin ├── deprecate │ ├── fast_search.py │ └── mcl_sparse.py ├── find_cluster.py ├── find_hit.py └── find_orth.py ├── deprecate ├── example │ ├── clean.sh │ ├── deprecate │ │ ├── add_taxon2fas.py │ │ └── chk.py │ ├── qry.fsa │ ├── ref.fsa │ ├── ref.fsa.operon │ └── run.sh ├── find_orth.py └── py27 │ ├── bin │ ├── deprecate │ │ ├── fast_search.py │ │ └── mcl_sparse.py │ ├── find_cluster.py │ ├── find_hit.py │ └── find_orth.py │ ├── lib │ ├── deprecate │ │ ├── fsearch0.py │ │ ├── fsearch_fast.py │ │ ├── spmm.py │ │ ├── spmm.py.bk │ │ └── test.py │ └── fsearch.py │ └── scripts │ ├── README.md │ ├── deprecate │ ├── pangenome.py │ ├── rbh2phy.py.bk │ └── run_all.py.bk │ ├── flt_orthomcl.py │ ├── fsfdp.py │ ├── get_rbh.py │ ├── mcl_cmp.py │ ├── operon_cluster.py │ ├── orth2phy.py │ ├── pan_genome.py │ ├── rbh2phy.py │ └── run_all.py ├── example ├── clean.sh ├── deprecate │ ├── add_taxon2fas.py │ └── chk.py ├── qry.fsa ├── ref.fsa ├── ref.fsa.operon └── run.sh ├── 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