DisjointSet             Return single linkage clusters from
                        'PairSummaries' objects.
EstimateRearrangementScenarios
                        Estimate Genome Rearrangement Events with
                        Double Cut and Join Operations
ExtractBy               Extract and organize 'XStringSet's of sequences
                        represented in a 'PairSummaries' object.
FindSets                Find all single linkage clusters in an
                        undirected pairs list.
Generic                 Model for predicting PID based on k-mer
                        statistics
LinkedPairs-class       Tables of where syntenic hits link pairs of
                        genes
NucleotideOverlap       Tabulating Pairs of Genomic Sequences
PairSummaries           Summarize connected pairs in a LinkedPairs
                        object
SequenceSimilarity      Return a numeric value that represents the
                        similarity between two aligned sequences as
                        determined by a provided subsitution matrix.
SubSetPairs             Subset a "PairSummaries" object.
gffToDataFrame          Generate a DataFrame of gene calls from a gff3
                        file
