Algorithms

The Genome Context Viewer is a menagerie of algorithms. This page is an inventory of the algorithms. Its purpose is posterity, education, and to help the developers remember what in the world these algorithms do and where they live.

Alignment

• Smith-Waterman
• Repeat
• Multiple alignment by profile hierarchical hidden Markov model training

Clustering

• Agglomerative hierarchical clustering

Collections

• Disjoint-set (union-find)

Distance Metrics

• Levenshtein
• Multiset Jaccard with support for k-mers and reversals

Intervals

• Greedy interval scheduling
• Weighted interval scheduling dynamic program

Sequence Analysis

• Breakpoint reversal sort

Synteny

• Fixed-radius near neighbors (islands and gaps)
• DAGchainer/MCScanX