├── .github └── workflows │ └── ci.yml ├── CITATION.cff ├── Cargo.toml ├── LICENSE ├── README.md ├── example └── data │ ├── Brachyspira_pilosicoli.fa │ ├── Gracilinema_caldarium.fa │ ├── Leadbettera_azotonutricia.fa │ ├── Leptonema_illini.fa │ ├── Leptospira_biflexa.fa │ ├── Leptospira_fluminis.fa │ ├── Leptospira_idonii.fa │ ├── Leptospira_interrogans.fa │ ├── Oceanispirochaeta_crateris.fa │ ├── Oceanispirochaeta_sp_M1.fa │ ├── Salinispira_pacifica.fa │ ├── Spirochaeta_africana.fa │ ├── Spirochaeta_isovalerica.fa │ ├── Thiospirochaeta_perfilievii.fa │ ├── Treponema_brennaborense.fa │ ├── Treponema_bryantii.fa │ ├── Treponema_denticola.fa │ ├── Treponema_maltophilum.fa │ ├── Treponema_pallidum.fa │ ├── Treponema_phagedenis.fa │ ├── Treponema_porcinum.fa │ ├── Treponema_primitia.fa │ ├── Treponema_rectale.fa │ ├── Treponema_ruminis.fa │ ├── Treponema_saccharophilum.fa │ ├── Treponema_sp_J25.fa │ ├── Treponema_sp_JC4.fa │ ├── Treponema_sp_Marseille-Q3903.fa │ ├── Treponema_sp_Marseille-Q4132.fa │ └── Treponema_succinifaciens.fa ├── path.cfg └── src ├── envs ├── error_handler.rs ├── mod.rs └── variables.rs ├── main.rs ├── modules ├── cluster.rs ├── config.rs ├── createdb.rs ├── genetree.rs ├── mod.rs ├── profile.rs ├── search.rs ├── tree.rs └── version.rs ├── seq ├── afdb_lookup.rs ├── combine_fasta.rs ├── create_gene_specific_fasta.rs ├── fasta_io.rs └── mod.rs ├── util ├── arg_parser.rs ├── checkpoint.rs ├── command.rs ├── message.rs └── mod.rs └── workflow ├── easy_core.rs ├── easy_search.rs └── mod.rs /.github/workflows/ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/steineggerlab/unicore/HEAD/.github/workflows/ci.yml -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/steineggerlab/unicore/HEAD/CITATION.cff 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