| as.data.frame.simMat | Similarity Matrices |
| as.matrix.simMat | Similarity Matrices |
| as.simMat | Similarity Matrices |
| as.simMat.matrix | Similarity Matrices |
| as.simMat.vector | Similarity Matrices |
| Behdenna.ProtWeaver | Presence/Absence Predictions for ProtWeaver |
| 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 |
| Coloc.ProtWeaver | Co-localization Predictions for ProtWeaver |
| ContextTree.ProtWeaver | Distance Matrix Predictions for ProtWeaver |
| Diag | Similarity Matrices |
| Diag.simMat | Similarity Matrices |
| Diag<- | Similarity Matrices |
| Diag<-.simMat | Similarity Matrices |
| DisjointSet | Return single linkage clusters from 'PairSummaries' objects. |
| DPhyloStatistic | D-Statistic for Binary States on a Phylogeny |
| 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 |
| EstimateRearrangementScenarios | Estimate Genome Rearrangement Events with Double Cut and Join Operations |
| 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. |
| GainLoss.ProtWeaver | Presence/Absence Predictions for ProtWeaver |
| GeneralizedRF | Information-Theoretic Generalized Robinson-Foulds Distance |
| Generic | Model for predicting PID based on k-mer statistics |
| gffToDataFrame | Generate a DataFrame of gene calls from a gff3 file |
| Hamming.ProtWeaver | Presence/Absence Predictions for ProtWeaver |
| Jaccard.ProtWeaver | Presence/Absence Predictions for ProtWeaver |
| LinkedPairs-class | Tables of where syntenic hits link pairs of genes |
| MirrorTree.ProtWeaver | Distance Matrix Predictions for ProtWeaver |
| MutualInformation.ProtWeaver | Presence/Absence Predictions for ProtWeaver |
| NucleotideOverlap | Tabulating Pairs of Genomic Sequences |
| PairSummaries | Summarize connected pairs in a LinkedPairs object |
| plot.ProtWeb | Plot predictions in a ProtWeb object |
| predict.ProtWeaver | Make predictions with ProtWeaver objects |
| print.LinkedPairs | Tables of where syntenic hits link pairs of genes |
| print.simMat | Similarity Matrices |
| ProfDCA.ProtWeaver | Presence/Absence Predictions for ProtWeaver |
| ProtWeaver | ProtWeaver: Predicting Protein Functional Association Networks |
| ProtWeaver-class | 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 |
| ProtWeaver-utils | ProtWeaver: Predicting Protein Functional Association Networks |
| ProtWeb | ProtWeb: Predictions from ProtWeaver |
| ResidueMI.ProtWeaver | Residue Based Predictions for 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. |
| simMat | Similarity Matrices |
| simMat-class | Similarity Matrices |
| SubSetPairs | Subset a "PairSummaries" object. |
| SuperTree | Create a Species Tree from Gene Trees |
| SuperTreeEx | Example Dendrograms |
| [.LinkedPairs | Tables of where syntenic hits link pairs of genes |