├── .gitignore ├── CHANGELOG.md ├── INDEX_FORMAT_CHANGELOG.tsv ├── LICENSE ├── README.md ├── demo ├── README.md ├── ass2species.map ├── bench │ ├── b.amr.fasta │ ├── b.gene_E_coli_16S.fasta │ ├── b.gene_E_faecalis_SecY.fasta │ └── b.plasmid_pCUVET18-1784.4.fasta ├── files.txt ├── prefix.hist.png ├── q.gene.fasta ├── q.gene.fasta.lexicmap.tsv ├── q.long-reads.fasta.gz ├── q.prophage.fasta ├── q.prophage.fasta.lexicmap.tsv ├── refs │ ├── GCF_000006945.2.fa.gz │ ├── GCF_000017205.1.fa.gz │ ├── GCF_000148585.2.fa.gz │ ├── GCF_000392875.1.fa.gz │ ├── GCF_000742135.1.fa.gz │ ├── GCF_001027105.1.fa.gz │ ├── GCF_001096185.1.fa.gz │ ├── GCF_001457655.1.fa.gz │ ├── GCF_001544255.1.fa.gz │ ├── GCF_002949675.1.fa.gz │ ├── GCF_002950215.1.fa.gz │ ├── GCF_003697165.2.fa.gz │ ├── GCF_006742205.1.fa.gz │ ├── GCF_009759685.1.fa.gz │ └── GCF_900638025.1.fa.gz ├── taxid.map └── taxonomy.tsv ├── docs ├── archetypes │ └── default.md ├── content │ ├── _index.md │ ├── faqs │ │ └── _index.md │ ├── installation │ │ └── _index.md │ ├── introduction │ │ └── _index.md │ ├── logo.svg │ ├── notes │ │ ├── _index.md │ │ └── motivation.md │ ├── performance@genbank.tsv │ ├── performance@genbank.tsv.sh │ ├── releases │ │ └── _index.md │ ├── tutorials │ │ ├── _index.md │ │ ├── index │ │ │ ├── _index.md │ │ │ ├── parameters-batches.tsv │ │ │ ├── parameters-general.tsv │ │ │ ├── parameters-masks.tsv │ │ │ └── parameters-seeds.tsv │ │ ├── misc │ │ │ ├── _index.md │ │ │ ├── index-allthebacteria.md │ │ │ ├── index-genbank.md │ │ │ ├── index-globdb.md │ │ │ ├── index-gtdb.md │ │ │ └── index-uhgg.md │ │ ├── parameters-align.tsv │ │ ├── parameters-general.tsv │ │ ├── parameters-limit-taxids.tsv │ │ ├── parameters-seeding.tsv │ │ └── search.md │ └── usage │ │ ├── _index.md │ │ ├── index │ │ └── _index.md │ │ ├── lexicmap.md │ │ ├── search.md │ │ └── utils │ │ ├── 2blast.md │ │ ├── _index.md │ │ ├── edit-genome-ids.md │ │ ├── genomes.md │ │ ├── kmers.md │ │ ├── masks.md │ │ ├── merge-search-results.md │ │ ├── reindex-seeds.md │ │ ├── remerge.md │ │ ├── seed-pos.md │ │ └── subseq.md ├── data │ └── menu │ │ ├── extra.yaml │ │ └── more.yaml ├── hugo.toml └── static │ ├── AllTheBacteria-v0.2.url.txt │ ├── GCF_000017205.1.png │ ├── GCF_000017205.1.seed_number.png │ ├── GCF_000392875.1.png │ ├── GCF_000392875.1.seed_number.png │ ├── GCF_002949675.1.png │ ├── GCF_002949675.1.seed_number.png │ ├── custom.css │ ├── favicon │ ├── android-chrome-192x192.png │ ├── android-chrome-512x512.png │ ├── apple-touch-icon.png │ ├── browserconfig.xml │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ ├── favicon-48x48.png │ ├── favicon.ico │ ├── favicon.svg │ ├── mstile-144x144.png │ ├── mstile-150x150.png │ ├── mstile-310x150.png │ ├── mstile-310x310.png │ ├── mstile-70x70.png │ ├── safari-pinned-tab.svg │ └── site.webmanifest │ ├── indexing.svg │ ├── logo.svg │ ├── overview.svg │ ├── prefix.hist.png │ └── searching.svg ├── go.mod ├── go.sum ├── lexicmap ├── .gitignore ├── build.sh ├── cmd │ ├── 2blast.go │ ├── autocomplete.go │ ├── edit-genome-ids.go │ ├── genome │ │ ├── genome.go │ │ └── genome_test.go │ ├── genomes.go │ ├── index.go │ ├── kmers.go │ ├── kv │ │ ├── kv-data.go │ │ ├── kv-data_test.go │ │ ├── kv-encoding.go │ │ ├── kv-reader.go │ │ ├── kv-searcher.go │ │ └── kv-searcher2.go │ ├── lib-chaining.go │ ├── lib-chaining2.go │ ├── lib-chaining3.go │ ├── lib-chaining_test.go │ ├── lib-index-build.go │ ├── lib-index-merge.go │ ├── lib-index-search-util.go │ ├── lib-index-search.go │ ├── lib-seq_compare.go │ ├── lib-seq_compare_test.go │ ├── masks.go │ ├── merge-search-results.go │ ├── re-merge.go │ ├── recount-bases.go │ ├── reindex-seeds.go │ ├── root.go │ ├── search.go │ ├── seed-pos.go │ ├── seedposition │ │ ├── seed_position.go │ │ └── seed_position_test.go │ ├── subseq.go │ ├── tree │ │ ├── tree.go │ │ └── tree_test.go │ ├── util-cli.go │ ├── util-io.go │ ├── util-logging.go │ ├── util.go │ ├── util │ │ ├── kmers.go │ │ ├── kmers_test.go │ │ 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