CRE_conservativity      Calculate cumulative relative entropy score
D_matrix                Calculate substitution rate matrix between two
                        amino acids
Escore_conservativity   Calculate the Escore conservation metric
RealValET_conservativity
                        Calculate real-value Evolutionary Trace (ET)
align_params            Get alignment dimensions
align_seq_mtx2grs       Convert amino acid symbols to groups according
                        to their properties of user's choice.
alignment               Sample alignment of soluable epoxide hydrolase
                        family
alignment2matrix        Load alignment into matrix
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
delete_isoforms         Delete protein isoforms from alignment object
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_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_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
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
