sitePath

sitePath clusters DNA/protein sequences using site polymorphism and their corresponding phylogenetic trees, employing a branch-and-bound like algorithm to minimize entropy representing the purity of site polymorphism of each cluster.

Key Features:

• Phylogeny-guided clustering: Clusters sequences by considering their location on the phylogenetic tree, restricting clustering to structurally adjacent sequences.
• Entropy minimization: Uses a branch-and-bound like algorithm to minimize the entropy representing the purity of site polymorphism of each cluster.
• Site polymorphism handling: Addresses the limitation that sequences with the same polymorphism on a single site may be genetically distant by incorporating tree structure.

Scientific Applications:

• Sequence clustering: Groups DNA or protein sequences based on site polymorphism patterns while accounting for phylogenetic relationships.
• Phylogenetic analysis: Identifies clusters of sequences that are both structurally adjacent on a tree and optimized for site polymorphism purity.

Methodology:

A branch-and-bound like algorithm minimizes the entropy representing the purity of site polymorphism of each cluster, with clustering restricted to structurally adjacent sequences on the phylogenetic tree.