CnCs                    Synonymous and Non-Synonymous Codon Match
                        Counts
aboutQueeems            References Relevant to the 'queeems' Package
baseFrequency           Counts Indicating Protein Base Prevalence
baseSummary-class       Protein Base Composition Numerics
bstringCodons           Convert a BStringSet Object to Codon Sequences
citing-class            Useful Package Citations
cncsentropy             Global [Non-]Synonymous Entropy Index for
                        Protein Sequence
cncsframe-class         Synonymous and Non-Synonymous Frequencies
codonDissimilarity      Codon Census Matrix Matched by Nucleotide
                        Dissimilarity
codondifferindex        Molecular Entropy Estimated from Codon
                        Mismatches
diffNucBinary           Compare Codon Pairs to Identify Nucleotide
                        Mismatch
entropyindex            Obtain Entropy Indices
fubarweights            FUBAR-like Weights
geneindex-class         Protein Information Entropy Handling
mnomLogl                Approximate Log-Likelihood of a Multinomial
                        Variable
molentropy              Molecular Entropy Generated Independently per
                        Base Site
n2cFreqs                Generate Codon Frequencies from Nucleotide
                        Frequencies
nonSynonymous           Identify Synonymous and Non-Synonymous Codons
queeems                 Quantify the Extent of Evolutionary Evidence in
                        Molecular Sequences
queeemsExtdata          Paths to Example Protein Sequence Files
saturateBF-class        Substitution Saturation Output: Bayesian
                        Paradigm
seqSaturation           Estimate Saturation Index For Protein Data
seqfilter               Delete Subset of Molecular Sequences
siteindices-class       Molecular Information Entropy Processor
softmax                 Softmax Transformation
