BlastSeqs               Run BLAST queries from R
BlockExpansion          Attempt to expand blocks of paired features in
                        a 'PairSummaries' object.
BlockReconciliation     Rejection scheme for asyntenic predicted pairs
BuiltInEnsembles        Pretrained ProtWeaver Ensemble Models
DPhyloStatistic         D-Statistic for Binary States on a Phylogeny
DisjointSet             Return single linkage clusters from
                        'PairSummaries' objects.
Endosymbionts_GeneCalls
                        Example genecalls
Endosymbionts_LinkedFeatures
                        Example synteny links
Endosymbionts_Pairs01   Example predicted pairs
Endosymbionts_Pairs02   Example predicted pairs
Endosymbionts_Pairs03   Example predicted pairs
Endosymbionts_Sets      A list of disjoint sets.
Endosymbionts_Synteny   A synteny object
EstimRearrScen          Estimate Genome Rearrangement Events with
                        Double Cut and Join Operations
ExampleStreptomycesData
                        Example ProtWeaver Input Data from
                        _Streptomyces_ Species
ExtractBy               Extract and organize 'DNAStringSets's.
FindSets                Find all single linkage clusters in an
                        undirected pairs list.
GeneralizedRF           Information-Theoretic Generalized
                        Robinson-Foulds Distance
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
ProtWeaver              ProtWeaver: Predicting Protein Functional
                        Association Networks
ProtWeaver-ColocPreds   Co-localization Predictions for ProtWeaver
ProtWeaver-DMPreds      Distance Matrix Predictions for ProtWeaver
ProtWeaver-PAPreds      Presence/Absence Predictions for ProtWeaver
ProtWeaver-ResiduePreds
                        Residue Based Predictions for ProtWeaver
ProtWeb                 ProtWeb: Predictions from ProtWeaver
RFDist                  Robinson-Foulds Distance
SelectByK               Predicted pair trimming using K-means.
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.
SuperTree               Create a Species Tree from Gene Trees
SuperTreeEx             Example Dendrograms
gffToDataFrame          Generate a DataFrame of gene calls from a gff3
                        file
plot.ProtWeb            Plot predictions in a ProtWeb object
predict.ProtWeaver      Make predictions with ProtWeaver objects
simMat                  Similarity Matrices
