function,replacement
DEPRECATED,None
vrna_aln_consensus_sequence,my_aln_consensus_sequence
vrna_aln_consensus_mis,my_aln_consensus_mis
vrna_aln_mpi,my_aln_mpi
vrna_aln_pscore,my_aln_pscore
vrna_aln_conservation_struct,my_aln_conservation_struct
vrna_aln_conservation_col,my_aln_conservation_col
vrna_maximum_matching_simple,my_maximum_matching
vrna_enumerate_necklaces,my_enumerate_necklaces
vrna_rotational_symmetry_pos,my_rotational_symmetry
vrna_boustrophedon,boustrophedon
vrna_file_commands_read,my_file_commands_read
vrna_sc_mod_read_from_jsonfile,my_sc_mod_read_from_jsonfile
vrna_sc_mod_read_from_json,my_sc_mod_read_from_json
duplexfold,my_duplexfold
duplex_subopt,my_duplex_subopt
aliduplexfold,my_aliduplexfold
aliduplex_subopt,my_aliduplex_subopt
vrna_eval_structure_simple_v,my_eval_structure_simple
vrna_eval_circ_structure_v,my_eval_circ_structure
vrna_eval_gquad_structure_v,my_eval_gquad_structure
vrna_eval_circ_gquad_structure_v,my_eval_circ_gquad_structure
vrna_eval_structure_pt_simple_v,my_eval_structure_pt_simple
vrna_file_SHAPE_read,my_file_SHAPE_read
vrna_file_fasta_read_record,my_file_fasta_read
vrna_file_RNAstrand_db_read_record,my_file_RNAstrand_db_read_record
vrna_file_connect_read_record,my_file_connect_read_record
vrna_file_msa_detect_format,my_file_msa_detect_format
vrna_file_msa_read,my_file_msa_read
vrna_file_msa_read_record,my_file_msa_read_record
vrna_file_msa_write,my_file_msa_write
vrna_heat_capacity_simple,my_heat_capacity
inverse_fold,my_inverse_fold
inverse_pf_fold,my_inverse_pf_fold
vrna_fold,my_fold
vrna_alifold,my_alifold
vrna_cofold,my_cofold
vrna_circfold,my_circfold
vrna_circalifold,my_circalifold
vrna_Lfoldz,my_Lfoldz
vrna_Lfold,my_Lfold
vrna_aliLfold,my_aliLfold
vrna_params_load,my_params_load
vrna_params_save,my_params_save
vrna_params_load_from_string,my_params_load_from_string
vrna_pf_add,my_pf_add
vrna_MEA_from_plist,my_MEA_from_plist
vrna_path_options_findpath,my_path_options_findpath
vrna_pfl_fold,my_pfl_fold
vrna_pfl_fold_up,pfl_fold_up
vrna_plot_coords,get_xy_coordinates
vrna_file_PS_aln_slice,file_PS_aln
vrna_plot_dp_EPS,plot_dp_EPS
vrna_seq_encode,my_seq_encode
vrna_db_from_ptable,my_db_from_ptable
vrna_db_flatten,db_flatten
vrna_db_from_WUSS,db_from_WUSS
vrna_abstract_shapes,abstract_shapes
vrna_ptable_from_string,my_ptable
vrna_pt_pk_get,my_ptable_pk
vrna_pt_pk_remove,my_pt_pk_remove
vrna_plist,my_plist
vrna_db_from_plist,db_from_plist
vrna_db_pk_remove,db_pk_remove
vrna_db_to_tree_string,db_to_tree_string
vrna_tree_string_unweight,tree_string_unweight
vrna_tree_string_to_db,tree_string_to_db
vrna_loopidx_from_ptable,my_loopidx_from_ptable
vrna_hx_from_ptable,my_hx_from_ptable
vrna_bp_distance,my_bp_distance
vrna_dist_mountain,my_dist_mountain
vrna_hamming_distance,my_hamming
vrna_hamming_distance_bound,my_hamming_bound
vrna_strtrim,my_strtrim
vrna_filename_sanitize,my_filename_sanitize