Calculate_Row_Weights   Calculate the sequence weights for all the rows
                        in my amino,using label as the grouping
Henikoff_weights        Calculates Henikoff weights for each sequence
                        in a binary amino acid matrix
LDH                     LDH alignment read in from a file
LDH.aap                 AAP matrix
LDH.aap.ave             AAP matrix
LDH.amino               Binary amino acid matrix after converting the
                        Lactate alignment
LDH.amino.gapless       Amino acid matrix after removing gaps
LDH.amino.pseudo        Amino acid matrix after adding pseudo counts
LDH.groups              Groups in the LDH alignment
Weight_Amino            Calculates sequence weight for each sequence in
                        an amino acid matrix
add_pseudo_counts       Add pseudo counts to amino acid matrix based on
                        defined groups
amino_counts            calculate count of amino acid types at each
                        position
average_cols_aap        Replaces gaps with the average of the column
bgafun                  BGAfun A method to identify specifity
                        determining residues in protein families
calculate_pseudo        Calculates pseudo count for each column in the
                        amino acid matrix
convertAAP-package      Converts an alignment into a matrix using the
                        AAP encoding
convert_aln_AAP         Converts alignment into a matrix using the
                        amino acid property encoding
convert_aln_amino       Converts an alignment object into binary amino
                        matrix
convert_amino-package   The functions required to convert an alignment
                        into a binary matrix suitable for BGA analysis
convert_seq_amino       Converts a single seqeunce into a binary string
create_colnames_amino   Creates the column names for the binary matrix
create_probab           Generates probability matrix for pseudocounts
                        calculation
create_profile          Creates a sequence profile for an binary amino
                        acid matrix
create_profile_strings
                        Create a profile string for each group in an
                        alignment
pseudo_counts           Calculate pseudo counts for a profile
remove_gaps             Removes gaps from a amino binary matrix
remove_gaps_groups      remove gaps from a binary amino matrix
run_between_pca         run PCA to identify functional positions in an
                        alignment
sum_20_aln              Calculates number of amino acids in each group
                        of 20 columns (1 column in an alignment)
sum_20_cols             Calculate number of amino acids in a column of
                        an alignment
sum_aln                 Calculate number of amino acids in each
                        position in an alignment
top_residues_2_groups   Return a list of the top residues at either end
                        of the axis
