Decile.Plot             VLF Decile Plot
Error.Rate              Error Rate
MODE                    Modal Sequence
MODE.freq               Modal Frequencies
MODE.second.freq        Second Modal Frequency
Sliding.Window          Sliding Window
VLF-package             Frequency Matrix Approach for Assessing Very
                        Low Frequency Variants in Sequence Records
VLF.aminoAcids          Amino Acid VLFs
VLF.convert.matrix      VLF Matrix Convert
VLF.count.pos           VLF Count for Sequence Positions
VLF.count.spec          VLF Count for Specimens
VLF.nucleotides         Nucleotide VLF Convert
VLF.reduced             Reduced VLF Matrix
aa.MODE                 Amino Acid Modal Sequence
aa.MODE.freq            Amino Acid Modal Frequencies
aa.MODE.second.freq     Amino Acid Second Modal Frequency
aa.VLF.convert.matrix   Convert Amino Acid Matrix
aa.VLF.count.pos        VLF position count
aa.VLF.count.spec       VLF Specimen Count
aa.VLF.reduced          Amino Acid Reduced
aa.compare              Amino Acid Comparison
aa.conservation_first   First Modal Amino Acid Conservation
aa.conservation_two     First and Second Modal Amino Acid Conservation
aa.count.function       Amino Acid Count
aa.find.singles         Find amino acid singles
aa.frequency.matrix.function
                        Amino Acid Frequency Matrix
aa.specimen.frequencies
                        Specimen Nucleotide Frequencies
aaVLFs.to.modalchanges
                        Amino Acid Changes
aminoAcid.matching.positions
                        Matching Amino Acid Positions
aminoAcidFun            Amino Acid VLF Analysis Function
birds                   Bird Nucleotide Sequences
birds_aminoAcids        Bird Amino Acid Sequences
compare                 Compare VLFs within Species
concordanceFun          VLF Concordance Check Function
concordant.to.modalchanges
                        Concordant Residue Changes
conservation_first      First Modal Conserved
conservation_two        First and Second Modal Conserved
count.function          Nucleotide Count
fasta.read              Read Fasta Files
ffrequency.matrix.function
                        Frequency Matrix
find.matching           Find Matching ntVLF and aaVLF Specimen.
find.singles            Single and Shared VLF Find
matched.codon.position
                        Codon Position of Matching aa and ntVLFs
nucleotide.matching.positions
                        Matching Nucleotide Positions
overall.matched         Final Matching
separate                Separate Specimen by Species Names
specimen.frequencies    Specimen Nucleotide Frequencies
vlfFun                  Nucleotide VLF Assessment Function
