Command-line reference

Generated from the commands' parsers by scripts/docs/cli_reference.py. domainator <command> --help shows the same options.

Annotate and search sequences and structures

domainate: Annotate contigs or proteins with reference hits, retaining records without hits.
domain_search: Select matching sequence records or hit neighborhoods; optionally translate CDS hits.
find_features: Annotate transmembrane regions, signal peptides, and other sequence features.
structure_domainate: Annotate structure-derived protein records, retaining records without hits.
structure_search: Select matching structure-derived protein records and mark their best-hit regions.

clean_sequences: Clean sequence names and residues, and filter out sequences with non-canonical residues.
color_genbank: Add color qualifiers to CDS and domain features.
deduplicate_genbank: Reduce redundancy by clustering sequences (cd-hit, usearch, diamond, or exact hashes).
extract_domains: Extract annotated domains as their own records.
extract_peptides: Extract translated CDSs as protein records, keeping their domain annotations.
extract_unannotated: Extract the regions of proteins not covered by any domain annotation.
filter_domains: Filter domain annotations by e-value, overlap, database, or name.
rotate_contigs: Set the origin of circular contigs relative to a domain.
select_by_cds: Extract contigs or neighborhoods around selected CDSs.
select_by_contig: Select whole contigs by their domain content and other properties.
select_by_coord: Extract contig regions listed in a coordinate table.
sort_contigs: Sort contigs by their Domain_Search score.
trim_contigs: Trim the ends of contigs.

hmmer_build: Build an HMM profile from a multiple sequence alignment.
infernal_build: Build a covariance model (CM) from a multiple sequence alignment (experimental).
hmmer_select: Extract a subset of profiles from HMM files.
hmmer_search: Select HMM profiles by their similarity to reference profiles.
hmmer_compare: Score and align pairs of HMM profiles.

seq_dist: Compute similarity scores between sequences or profiles.
kmer_dist: Compute exact k-mer similarity scores between sequence records.
structure_dist: Compute similarity or distance matrices between protein structures.
compare_contigs: Compute similarities between gene neighborhoods from their domain content and order.
transform_matrix: Convert score matrices into normalized scores or distances.

build_ssn: Build a sequence similarity network for Cytoscape or the Domainator Viewer.
ssn_navigator: Query a similarity network bundle: clusters, members, and metadata.
split_by_cluster: Split a sequence or profile file into one file per cluster of a similarity matrix.
build_tree: Build a UPGMA tree from a distance or similarity matrix.
build_projection: Project a matrix into 2D or 3D with UMAP, t-SNE, or PCA.
viewer: Write the Domainator Viewer, empty or opening a network, tree, or projection bundle.