AAcompare               Comparing viral quasispecies diversity metrics
                        at amino acid level
filtfast                Filtering highly dissimilar reads/sequences out
                        of the alignment
gapremove               Removing gap-rich positions and/or
                        reads/sequences
otucompare              Comparing operational taxonomic unit (OTU) by
                        k-means clustering between samples
pctopt                  Optimizing cut-off percentage for noise
                        minimization
snvcompare              Plotting single nucleotide variant (SNV)
                        frequency in read alignment across different
                        samples
vqsassess               Sequencing error and noise minimization, read
                        down-sampling, and data preparation for viral
                        quasispecies comparison
vqscompare              Comparing viral quasispecies profile and
                        operational taxonomic unit (OTU) classified by
                        k-means clustering between samples
vqscustompct            Sequencing error and noise minimization with
                        customized % cut-off at particular nucleotide
                        region, read down-sampling, and data
                        preparation for viral quasispecies comparison
vqsout                  Exporting viral quasispecies profile comparison
                        results
vqsresub                Computing viral quasispecies diversity metrics
                        of noise-minimized repeatedly down-sampled read
                        alignments
vqssub                  Computing viral quasispecies diversity metrics
                        of noise-minimized down-sampled read alignment
