# Tools for Working With Synteny Objects

## Documentation for package ‘SynExtend’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
CIDist | Clustering Information Distance
CIDist_NullDist | Simulated Null Distributions for CI Distance
Coloc.ProtWeaver | Co-localization Predictions for ProtWeaver
ContextTree.ProtWeaver | Distance Matrix Predictions for ProtWeaver
CorrGL.ProtWeaver | Presence/Absence Predictions for ProtWeaver
dendrapply | Apply a Function to All Nodes of a Dendrogram
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
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
JRFDist | Jaccard-Robinson-Foulds Distance
KFDist | Kuhner-Felsenstein Distance
LinkedPairs-class | Tables of where syntenic hits link pairs of genes
MirrorTree.ProtWeaver | Distance Matrix Predictions for ProtWeaver
MoransI | Moran's _I_ Spatial Autocorrelation Index
MutualInformation.ProtWeaver | Presence/Absence Predictions for ProtWeaver
NucleotideOverlap | Tabulating Pairs of Genomic Sequences
PairSummaries | Summarize connected pairs in a LinkedPairs object
PhyloDistance | Calculate Distance between Unrooted Phylogenies
PhyloDistance-CI | Clustering Information Distance
PhyloDistance-JRF | Jaccard-Robinson-Foulds Distance
PhyloDistance-KF | Kuhner-Felsenstein Distance
PhyloDistance-RF | Robinson-Foulds Distance
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 Level Predictions for ProtWeaver
ProtWeaver-utils | ProtWeaver: Predicting Protein Functional Association Networks
ProtWeb | ProtWeb: Predictions from ProtWeaver
ResidueMI.ProtWeaver | Residue Level 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
SpeciesTree | ProtWeaver: Predicting Protein Functional Association Networks
SpeciesTree.ProtWeaver | ProtWeaver: Predicting Protein Functional Association Networks
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