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
CheckAgainstReport      Pull an assembly from the NCBI FTP site.
CIDist_NullDist         Simulated Null Distributions for CI Distance
CreateDecoys            Generating Decoy Alignments for Feature Pairs
DecisionTree-class      Decision Trees for Random Forests
dendrapply              Apply a Function to All Nodes of a Dendrogram
DisjointSet             Return single linkage clusters from
                        'PairSummaries' objects.
DPhyloStatistic         D-Statistic for Binary States on a Phylogeny
EstimateExoLabel        Estimate ExoLabel Disk Consumption
EstimRearrScen          Estimate Genome Rearrangement Scenarios with
                        Double Cut and Join Operations
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
genecalls               Example genecall data
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.
init_pairs              Example genecall data
linked_features         Example genecall data
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
plot.EvoWeb             Plot predictions in a EvoWeb object
predict.EvoWeaver       Make predictions with EvoWeaver objects
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.
simMat                  Similarity Matrices
SquaregffBy             Convert a GRanges object to a DataFrame
subset.dendrogram       Subsetting dendrogram objects
SummarizePairs          Summarizing Linked Feature Pairs from a
                        LinkedPairs Object
SuperTree               Create a Species Tree from Gene Trees
SuperTreeEx             Example Dendrograms
syn                     Example genecall data
ToFeatureSpace          Tabulating Features Linked by Syntenic Hits
