Index

C

calculate_conservation() (in module pairk)

calculate_conservation_arrays() (in module pairk)

E

encode() (pairk.ESM_Model method)

ESM_Model (class in pairk)

F

fasta_MSA_to_idr_dict() (in module pairk.utilities) fasta_MSA_to_idr_map() (in module pairk.utilities) fasta_MSA_to_unaligned_sequences() (in module pairk.utilities)

FastaImporter (class in pairk) find_query_kmer_positions() (pairk.PairkAln method) (pairk.PairkConservation method) from_file() (pairk.PairkAln class method)

G

get_average_score() (pairk.PairkConservation method)

get_pseudo_alignment() (pairk.PairkAln method)

I

import_as_alignment() (pairk.FastaImporter method) import_as_dict() (pairk.FastaImporter method)

import_as_list() (pairk.FastaImporter method) import_as_str_dict() (pairk.FastaImporter method)

M

make_aligner() (in module pairk) module pairk.single_kmer pairk.utilities

P

pairk.single_kmer module pairk.utilities module pairk_alignment() (in module pairk) pairk_alignment_embedding_distance() (in module pairk) pairk_alignment_needleman() (in module pairk) pairk_alignment_single_kmer() (in module pairk.single_kmer)

PairkAln (class in pairk) PairkConservation (class in pairk) plot_background_distribution() (pairk.PairkConservation method) plot_conservation_mosaic() (pairk.PairkConservation method) plot_position_heatmap() (pairk.PairkAln method) plot_score_barplot() (pairk.PairkConservation method) plot_score_heatmap() (pairk.PairkAln method) plot_sequence_logo() (pairk.PairkConservation method) print_available_matrices() (in module pairk)

R

read_results_from_file() (pairk.PairkConservation class method)

W

write_results_to_file() (pairk.PairkConservation method)

write_to_file() (pairk.PairkAln method)