# Tools for Working With Synteny Objects

## Documentation for package ‘SynExtend’ version 1.14.0

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

## Help Pages

Ancestral.EvoWeaver | Sequence-Level Predictions for EvoWeaver
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.EvoWeaver | Phylogenetic Profiling Predictions for EvoWeaver
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 EvoWeaver Ensemble Models
CIDist | Clustering Information Distance
CIDist_NullDist | Simulated Null Distributions for CI Distance
Coloc.EvoWeaver | Gene Organization Predictions for EvoWeaver
ColocMoran.EvoWeaver | Gene Organization Predictions for EvoWeaver
ContextTree.EvoWeaver | Phylogenetic Structure Predictions for EvoWeaver
CorrGL.EvoWeaver | Phylogenetic Profiling Predictions for EvoWeaver
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
EvoWeaver | EvoWeaver: Predicting Protein Functional Association Networks
EvoWeaver-class | EvoWeaver: Predicting Protein Functional Association Networks
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
EvoWeaver-utils | EvoWeaver: Predicting Protein Functional Association Networks
EvoWeb | EvoWeb: Predictions from EvoWeaver
ExampleStreptomycesData | Example EvoWeaver Input Data from _Streptomyces_ Species
ExtractBy | Extract and organize 'DNAStringSets's.
FastQFromSRR | Get Sequencing Data from the SRA
FindSets | Find all single linkage clusters in an undirected pairs list.
FitchParsimony | Calculate ancestral states using Fitch Parsimony
GainLoss.EvoWeaver | Phylogenetic Profiling Predictions for EvoWeaver
Generic | Model for predicting PID based on k-mer statistics
gffToDataFrame | Generate a DataFrame of gene calls from a gff3 file
Hamming.EvoWeaver | Phylogenetic Profiling Predictions for EvoWeaver
Jaccard.EvoWeaver | Phylogenetic Profiling Predictions for EvoWeaver
JRFDist | Jaccard-Robinson-Foulds Distance
KFDist | Kuhner-Felsenstein Distance
LinkedPairs-class | Tables of where syntenic hits link pairs of genes
MakeBlastDb | Create a BLAST Database from R
MirrorTree.EvoWeaver | Phylogenetic Structure Predictions for EvoWeaver
MoransI | Moran's _I_ Spatial Autocorrelation Index
MutualInformation.EvoWeaver | Phylogenetic Profiling Predictions for EvoWeaver
NucleotideOverlap | Tabulating Pairs of Genomic Sequences
NVDT.EvoWeaver | Sequence-Level Predictions for EvoWeaver
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.EvoWeb | Plot predictions in a EvoWeb object
predict.EvoWeaver | Make predictions with EvoWeaver objects
print.LinkedPairs | Tables of where syntenic hits link pairs of genes
print.simMat | Similarity Matrices
ProfDCA.EvoWeaver | Phylogenetic Profiling Predictions for EvoWeaver
ResidueMI.EvoWeaver | Sequence-Level Predictions for EvoWeaver
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 | EvoWeaver: Predicting Protein Functional Association Networks
SpeciesTree.EvoWeaver | EvoWeaver: Predicting Protein Functional Association Networks
subset.dendrogram | Subsetting dendrogram objects
SubSetPairs | Subset a "PairSummaries" object.
SuperTree | Create a Species Tree from Gene Trees
SuperTreeEx | Example Dendrograms
TranscripMI.EvoWeaver | Gene Organization Predictions for EvoWeaver
TreeDistance.EvoWeaver | Phylogenetic Structure Predictions for EvoWeaver
[.LinkedPairs | Tables of where syntenic hits link pairs of genes