AAHitScoping            Adjust the scope of kmer hits between feature
                        and genome space.
ApproximateBackground   Return the approximate background alignment
                        score for a series of paired sequences.
BlastSeqs               Run BLAST queries from R
BlockByRank             Return simple summaries of blocks of candidate
                        pairs.
BuiltInEnsembles        Pretrained EvoWeaver Ensemble Models
CIDist_NullDist         Simulated Null Distributions for CI Distance
CheckAgainstReport      Pull an assembly from the NCBI FTP site.
CreateDecoys            Generating Decoy Alignments for Feature Pairs
DPhyloStatistic         D-Statistic for Binary States on a Phylogeny
DecisionTree-class      Decision Trees for Random Forests
DisjointSet             Return single linkage clusters from
                        'PairSummaries' objects.
EstimRearrScen          Estimate Genome Rearrangement Scenarios with
                        Double Cut and Join Operations
EstimateExoLabel        Estimate ExoLabel Disk Consumption
EvaluatePairs           Evaluating and Filtering Candidate Feature
                        Pairs Against Decoy Alignments
EvoWeaver               EvoWeaver: Identifying Gene Functional
                        Associations from Coevolutionary Signals
EvoWeaver-GOPreds       Gene Organization Predictions for EvoWeaver
EvoWeaver-PPPreds       Phylogenetic Profiling Predictions for
                        EvoWeaver
EvoWeaver-PSPreds       Phylogenetic Structure Predictions for
                        EvoWeaver
EvoWeaver-SLPreds       Sequence Level Predictions for EvoWeaver
EvoWeb                  EvoWeb: Predictions from EvoWeaver
ExampleStreptomycesData
                        Example EvoWeaver Input Data from
                        _Streptomyces_ Species
ExoLabel                ExoLabel: Out-of-Memory Fast Label Propagation
ExtractBy               Extract and organize 'DNAStringSets's.
FastQFromSRR            Get Sequencing Data from the SRA
FeaturesFromDF          Return a DNAStringSet of features
FindSets                Find all single linkage clusters in an
                        undirected pairs list.
FitchParsimony          Calculate ancestral states using Fitch
                        Parsimony
FrameDownward           Adjust a DataFrame of genecalls
Generic                 Model for predicting PID based on k-mer
                        statistics
GetTranslatedFeatures   Translate Nucleotide Features to Amino Acid
                        Sequences
HitConsensus            Return a numeric measure of whether kmer hits
                        linking two genomic features are in linearly
                        similar locations in both features.
LinkedPairs-class       Tables of where syntenic hits link pairs of
                        genes
MakeBlastDb             Create a BLAST Database from R
MoranI                  Moran's _I_ Spatial Autocorrelation Index
NormVec                 Unit normalize a vector
NucleotideOverlap       Tabulating Features Linked by Syntenic Hits
OneSite                 Calculate a site on a right hyperbola.
PhyloDistance           Calculate Distance between Unrooted Phylogenies
PhyloDistance-CI        Clustering Information Distance
PhyloDistance-JRF       Jaccard-Robinson-Foulds Distance and Nye
                        Similarity
PhyloDistance-KF        Kuhner-Felsenstein Distance
PhyloDistance-RF        Robinson-Foulds Distance
RandForest              Classification and Regression with Random
                        Forests
SequenceSimilarity      Return a numeric value that represents the
                        similarity between two aligned sequences as
                        determined by a provided subsitution matrix.
SquaregffBy             Convert a GRanges object to a DataFrame
SummarizePairs          Summarizing Linked Feature Pairs from a
                        LinkedPairs Object
SuperTree               Create a Species Tree from Gene Trees
SuperTreeEx             Example Dendrograms
ToFeatureSpace          Tabulating Features Linked by Syntenic Hits
dendrapply              Apply a Function to All Nodes of a Dendrogram
genecalls               Example genecall data
init_pairs              Example genecall data
linked_features         Example genecall data
plot.EvoWeb             Plot predictions in a EvoWeb object
predict.EvoWeaver       Make predictions with EvoWeaver objects
simMat                  Similarity Matrices
subset.dendrogram       Subsetting dendrogram objects
syn                     Example genecall data
