Entry: Calculate_Row_Weights
Aliases: Calculate_Row_Weights
Keywords: manip
Description: Calculate the sequence weights for all the rows in my amino,using label as the grouping
URL: ../../../library/bgafun/html/Calculate_Row_Weights.html

Entry: Henikoff_weights
Aliases: Henikoff_weights
Keywords: manip
Description: Calculates Henikoff weights for each sequence in a binary amino acid matrix
URL: ../../../library/bgafun/html/Henikoff_weights.html

Entry: LDH
Aliases: LDH
Keywords: IO
Description: LDH alignment read in from a file
URL: ../../../library/bgafun/html/LDH.html

Entry: LDH.aap
Aliases: LDH.aap
Keywords: datasets
Description: AAP matrix
URL: ../../../library/bgafun/html/LDH.aap.html

Entry: LDH.aap.ave
Aliases: LDH.aap.ave
Keywords: datasets
Description: AAP matrix
URL: ../../../library/bgafun/html/LDH.aap.ave.html

Entry: LDH.amino
Aliases: LDH.amino
Keywords: datasets
Description: Binary amino acid matrix after converting the Lactate alignment
URL: ../../../library/bgafun/html/LDH.amino.html

Entry: LDH.amino.gapless
Aliases: LDH.amino.gapless
Keywords: datasets
Description: Amino acid matrix after removing gaps
URL: ../../../library/bgafun/html/LDH.amino.gapless.html

Entry: LDH.amino.pseudo
Aliases: LDH.amino.pseudo
Keywords: datasets
Description: Amino acid matrix after adding pseudo counts
URL: ../../../library/bgafun/html/LDH.amino.pseudo.html

Entry: LDH.groups
Aliases: LDH.groups
Keywords: datasets
Description: Groups in the LDH alignment
URL: ../../../library/bgafun/html/LDH.groups.html

Entry: Weight_Amino
Aliases: Weight_Amino
Keywords: manip
Description: Calculates sequence weight for each sequence in an amino acid matrix
URL: ../../../library/bgafun/html/Weight_Amino.html

Entry: add_pseudo_counts
Aliases: add_pseudo_counts
Keywords: manip
Description: Add pseudo counts to amino acid matrix based on defined groups
URL: ../../../library/bgafun/html/add_pseudo_counts.html

Entry: amino_counts
Aliases: amino_counts
Keywords: manip
Description: calculate count of amino acid types at each position
URL: ../../../library/bgafun/html/amino_counts.html

Entry: average_cols_aap
Aliases: average_cols_aap
Keywords: IO
Description: Replaces gaps with the average of the column
URL: ../../../library/bgafun/html/average_cols_aap.html

Entry: BGAfun
Aliases: bgafun
Keywords: package
Description: BGAfun A method to identify specifity determining residues in protein families
URL: ../../../library/bgafun/html/bgafun.html

Entry: calculate_pseudo
Aliases: calculate_pseudo
Keywords: manip
Description: Calculates pseudo count for each column in the amino acid matrix
URL: ../../../library/bgafun/html/calculate_pseudo.html

Entry: convertAAP-package
Aliases: convertAAP-package convertAAP
Keywords: package
Description: Converts an alignment into a matrix using the AAP encoding
URL: ../../../library/bgafun/html/convertAAP.package.html

Entry: convert_aln_AAP
Aliases: convert_aln_AAP
Keywords: IO
Description: Converts alignment into a matrix using the amino acid property encoding
URL: ../../../library/bgafun/html/convert_aln_AAP.html

Entry: convert_aln_amino
Aliases: convert_aln_amino
Keywords: IO
Description: Converts an alignment object into binary amino matrix
URL: ../../../library/bgafun/html/convert_aln_amino.html

Entry: convert_amino-package
Aliases: convert_amino-package
Keywords: package
Description: The functions required to convert an alignment into a binary matrix suitable for BGA analysis
URL: ../../../library/bgafun/html/convert_amino.package.html

Entry: convert_seq_AAP
Aliases: convert_seq_AAP
Keywords: internal
Description: Convert sequence into string representing AAP values
URL: ../../../library/bgafun/html/convert_seq_AAP.html

Entry: convert_seq_amino
Aliases: convert_seq_amino
Keywords: IO
Description: Converts a single seqeunce into a binary string
URL: ../../../library/bgafun/html/convert_seq_amino.html

Entry: create_colnames_AAP
Aliases: create_colnames_AAP
Keywords: internal
Description: Create column names for an AAP matrix
URL: ../../../library/bgafun/html/create_colnames_AAP.html

Entry: create_colnames_amino
Aliases: create_colnames_amino
Keywords: manip
Description: Creates the column names for the binary matrix
URL: ../../../library/bgafun/html/create_colnames_amino.html

Entry: create_probab
Aliases: create_probab
Keywords: manip
Description: Generates probability matrix for pseudocounts calculation
URL: ../../../library/bgafun/html/create_probab.html

Entry: create_profile
Aliases: create_profile
Keywords: manip
Description: Creates a sequence profile for an binary amino acid matrix
URL: ../../../library/bgafun/html/create_profile.html

Entry: create_profile_strings
Aliases: create_profile_strings
Keywords: manip
Description: Create a profile string for each group in an alignment
URL: ../../../library/bgafun/html/create_profile_strings.html

Entry: pseudo_counts
Aliases: pseudo_counts
Keywords: manip
Description: Calculate pseudo counts for a profile
URL: ../../../library/bgafun/html/pseudo_counts.html

Entry: remove_gaps
Aliases: remove_gaps
Keywords: IO
Description: Removes gaps from a amino binary matrix
URL: ../../../library/bgafun/html/remove_gaps.html

Entry: remove_gaps_groups
Aliases: remove_gaps_groups
Keywords: manip
Description: remove gaps from a binary amino matrix
URL: ../../../library/bgafun/html/remove_gaps_groups.html

Entry: run_between_pca
Aliases: run_between_pca
Keywords: manip
Description: run PCA to identify functional positions in an alignment
URL: ../../../library/bgafun/html/run_between_pca.html

Entry: sum_20_aln
Aliases: sum_20_aln
Keywords: manip
Description: Calculates number of amino acids in each group of 20 columns (1 column in an alignment)
URL: ../../../library/bgafun/html/sum_20_aln.html

Entry: sum_20_cols
Aliases: sum_20_cols
Keywords: manip
Description: Calculate number of amino acids in a column of an alignment
URL: ../../../library/bgafun/html/sum_20_cols.html

Entry: sum_aln
Aliases: sum_aln
Keywords: manip
Description: Calculate number of amino acids in each position in an alignment
URL: ../../../library/bgafun/html/sum_aln.html

Entry: top_residues_2_groups
Aliases: top_residues_2_groups
Keywords: manip
Description: Return a list of the top residues at either end of the axis
URL: ../../../library/bgafun/html/top_residues_2_groups.html
