# Tools for Working With Synteny Objects

## Documentation for package ‘SynExtend’ version 1.6.0

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

## Help Pages

DisjointSet | Return single linkage clusters from 'PairSummaries' objects.
EstimateRearrangementScenarios | Estimate Genome Rearrangement Events with Double Cut and Join Operations
ExtractBy | Extract and organize 'XStringSet's of sequences represented in a 'PairSummaries' object.
FindSets | Find all single linkage clusters in an undirected pairs list.
Generic | Model for predicting PID based on k-mer statistics
gffToDataFrame | Generate a DataFrame of gene calls from a gff3 file
LinkedPairs-class | Tables of where syntenic hits link pairs of genes
NucleotideOverlap | Tabulating Pairs of Genomic Sequences
PairSummaries | Summarize connected pairs in a LinkedPairs object
print.LinkedPairs | Tables of where syntenic hits link pairs of genes
SequenceSimilarity | Return a numeric value that represents the similarity between two aligned sequences as determined by a provided subsitution matrix.
SubSetPairs | Subset a "PairSummaries" object.
[.LinkedPairs | Tables of where syntenic hits link pairs of genes