Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | W A align() (in module seqtree.pairwise) (seqtree.Index method) aligned_query (seqtree.Alignment property) aligned_ref (seqtree.Alignment property) Alignment (class in seqtree) alphabet_symbols() (in module seqtree) amino_acids() (in module seqtree) anchors (seqtree.layout.AnchorSpec attribute) AnchorSpec (class in seqtree.layout) assign_allele() (seqtree.pmhc.PMHCStore method) B best_score (seqtree.Candidate property) blosum45() (seqtree.SubstitutionMatrix static method) blosum62() (seqtree.SubstitutionMatrix static method) blosum80() (seqtree.SubstitutionMatrix static method) build() (seqtree.Index static method) (seqtree.KmerIndex static method) build_kmer_index() (in module seqtree.pmhc) C Candidate (class in seqtree) central_prior() (in module seqtree.gapblock) cls (seqtree.layout.AnchorSpec attribute) (seqtree.pmhc.EpitopeHit attribute) collisions_batch() (seqtree.Index method) consensus() (seqtree.gapblock.IslandProfile method) core_kmers() (in module seqtree.seeds) count() (seqtree.seeds.SeedIndex method) D deletion_variants() (in module seqtree.gapblock) dist_matrix() (in module seqtree.pairwise) E embed_in_frame() (in module seqtree.gapblock) engine (seqtree.SearchParams property) epitope (seqtree.pmhc.EpitopeHit attribute) EpitopeHit (class in seqtree.pmhc) evalue() (seqtree.seeds.SeedIndex method) evalues() (in module seqtree) F find_mimics() (in module seqtree.pmhc) fit() (seqtree.gapblock.IslandProfile class method) frame_prior() (in module seqtree.gapblock) from_index() (seqtree.seeds.SeedIndex class method) from_pmhc() (seqtree.pmhc.PMHCStore class method) from_records() (seqtree.pmhc.PMHCStore class method) from_similarity() (seqtree.SubstitutionMatrix static method) from_tables() (seqtree.PositionalMatrix static method) from_weights() (seqtree.PositionalMatrix static method) G gap_cost() (in module seqtree.gapblock) gap_extend (seqtree.SearchParams property) gap_open (seqtree.SearchParams property) gapblock_score() (in module seqtree.gapblock) GapBlockIndex (class in seqtree.gapblock) gather() (seqtree.seeds.SeedIndex method) gene (seqtree.pmhc.EpitopeHit attribute) H hamming() (in module seqtree.distance) hamming_matrix() (in module seqtree.distance) Hit (class in seqtree) I Index (class in seqtree) IslandProfile (class in seqtree.gapblock) K KmerIndex (class in seqtree) kmers() (in module seqtree.layout) L levenshtein() (in module seqtree.distance) levenshtein_matrix() (in module seqtree.distance) load() (seqtree.Index static method) (seqtree.KmerIndex static method) load_control() (in module seqtree) M mask_anchors() (in module seqtree.layout) masked() (seqtree.PositionalMatrix method) matrix (seqtree.SearchParams property) max_dels (seqtree.SearchParams property) max_ins (seqtree.SearchParams property) max_penalty (seqtree.SearchParams property) max_subs (seqtree.SearchParams property) max_total_edits (seqtree.SearchParams property) mhc (seqtree.pmhc.EpitopeHit attribute) mode (seqtree.SearchParams property) module seqtree.distance seqtree.gapblock seqtree.layout seqtree.pairwise seqtree.pmhc seqtree.seeds N n_dels (seqtree.Hit property) n_ins (seqtree.Hit property) n_subs (seqtree.Hit property) num_kmers() (seqtree.KmerIndex method) num_peptides() (seqtree.KmerIndex method) O ops (seqtree.Alignment property) P pairwise_batch() (in module seqtree) pam100() (seqtree.SubstitutionMatrix static method) pam250() (seqtree.SubstitutionMatrix static method) penalty() (seqtree.PositionalMatrix method) (seqtree.SubstitutionMatrix method) peptide_id (seqtree.Candidate property) PMHCStore (class in seqtree.pmhc) pos_matrix (seqtree.SearchParams property) PositionalMatrix (class in seqtree) positions_prior() (in module seqtree.gapblock) presentation_features() (in module seqtree.layout) profile_prior() (in module seqtree.gapblock) R ref_id (seqtree.Hit property) ref_seq() (seqtree.Index method) resolve() (seqtree.layout.AnchorSpec method) row() (seqtree.gapblock.ScoreMatrix method) S save() (seqtree.Index method) (seqtree.KmerIndex method) scale() (seqtree.SubstitutionMatrix method) score (seqtree.Alignment property) (seqtree.Hit property) (seqtree.pmhc.EpitopeHit attribute) score() (in module seqtree.pairwise) (seqtree.gapblock.IslandProfile method) score_batch() (seqtree.gapblock.IslandProfile method) score_matrix() (in module seqtree.gapblock) (in module seqtree.pairwise) ScoreMatrix (class in seqtree.gapblock) search() (seqtree.gapblock.GapBlockIndex method) (seqtree.Index method) search_batch() (seqtree.Index method) search_homologs() (seqtree.pmhc.PMHCStore method) search_top() (seqtree.Index method) SearchParams (class in seqtree) seed_and_gather() (seqtree.KmerIndex method) seed_evalues() (seqtree.seeds.SeedIndex method) SeedIndex (class in seqtree.seeds) seqtree.distance module seqtree.gapblock module seqtree.layout module seqtree.pairwise module seqtree.pmhc module seqtree.seeds module shape (seqtree.gapblock.ScoreMatrix property) shared_kmers (seqtree.Candidate property) (seqtree.pmhc.EpitopeHit attribute) significant() (seqtree.seeds.SeedIndex method) similarity() (seqtree.SubstitutionMatrix method) size() (seqtree.pmhc.PMHCStore method) (seqtree.PositionalMatrix method) (seqtree.SubstitutionMatrix method) spec_for() (in module seqtree.layout) spec_has_anchors() (in module seqtree.pmhc) species (seqtree.pmhc.EpitopeHit attribute) structural() (seqtree.SubstitutionMatrix static method) SubstitutionMatrix (class in seqtree) T thetas_from_scores() (in module seqtree) threshold_for_evalue() (in module seqtree) U union_evalue() (seqtree.seeds.SeedIndex method) unit() (seqtree.SubstitutionMatrix static method) W weight_profile() (in module seqtree.layout) width() (seqtree.PositionalMatrix method)