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| alignment | Sample alignment of soluable epoxide hydrolase family |
| alignment2matrix | Load alignment into matrix |
| align_params | Get alignment dimensions |
| align_seq_mtx2grs | Convert amino acid symbols to groups according to their properties of user's choice. |
| barplotshow | Shows barplot with amino acid variation on the specified position |
| calculate_AA_variation | Calculate AA variations on each position of the multiple sequence alignment |
| calculate_pseudo_counts | Calculate pseudo counts for alignment |
| compare_cons_metrics | compare_cons_metrics |
| cons2seqs_ident | Identity of each sequence in the alignment to the consensus sequence. |
| cons2seqs_sim | Group consensus to each sequence in the alignment similarity |
| consensus | Consensus sequence determination |
| convert_AA_symbol | Amino acids symbols conversion |
| create_final_CSV | Create CSV file to save results |
| create_structure_seq | Superimpose structural data of interest on sequence after the alignmment |
| CRE_conservativity | Calculate cumulative relative entropy score |
| delete_isoforms | Delete protein isoforms from alignment object |
| D_matrix | Calculate substitution rate matrix between two amino acids |
| Escore_conservativity | Calculate the Escore conservation metric |
| excl_low_prob_strcts | Exclude low probability structural data |
| find_consecutive_seq | Find sequences of numbers in a numeric vector |
| find_seq | Find sequence by id in alignment. |
| find_seqid | Find sequence identifier by other sequence identifier in given alignment within a specified library |
| get_pos_based_seq_weights | Get position based weights of sequences in alignment |
| get_prot_entropy | Get MSA-based calculated entropy for chosen protein. |
| get_remarks465_pdb | Get "REMARK 465" data from PDB file |
| get_seq_names | Get names of sequences from alignment |
| get_seq_weights | Get sequences weights |
| get_structures_entropy | Get entropy of amino acids (for region of interest) in given protein |
| get_structures_idx | Get IDs of structure(s) elements from aligned sequences (MSA) |
| gonnet | Gonnet substitution matrix |
| is_upper | Check if the letter is uppercase. |
| kabat_conservativity | Calculate Kabat conservation metric |
| kolmogorov_smirnov_test | Perform Kolmogorov-Smirnov test for structural data |
| landgraf_conservativity | Calculate Landgraf conservation score |
| noteworthy_seqs | Find noteworthy sequences in the dataset (aligned sequences) |
| pairwise_alignment_MSA | Calculate pairwise alignment for whole MSA |
| plot_entropy | Plot entropies for protein |
| plot_structure_on_protein | Plot structure entropy on protein background |
| prepare_structure_profile | This function combines the entropy data for structure building amino acids with their indices |
| preprocess_hmm_output | preprocess HMM output |
| read_structure | Read structure data from a text file |
| RealValET_conservativity | Calculate real-value Evolutionary Trace (ET) |
| schneider_conservativity | Calculate Schneider conservation metric |
| shannon_conservativity | Calculate Shannon conservation metric |
| small_alignment | Sample small alignment of soluable epoxide hydrolase family |
| structure | A sample structure data |
| substitution_mtx | Read a substitution matrix |