wuaipinglab/sitePath: Phylogeny-based sequence clustering with site polymorphism

Using site polymorphism is one of the ways to cluster DNA/protein sequences but it is possible for the sequences with the same polymorphism on a single site to be genetically distant. This package is aimed at clustering sequences using site polymorphism and their corresponding phylogenetic trees. By considering their location on the tree, only the structurally adjacent sequences will be clustered. However, the adjacent sequences may not necessarily have the same polymorphism. So a branch-and-bound like algorithm is used to minimize the entropy representing the purity of site polymorphism of each cluster.

Getting started

Package details

Bioconductor views Alignment MultipleSequenceAlignment Phylogenetics SNP Software
LicenseMIT + file LICENSE
URL https://wuaipinglab.github.io/sitePath/
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
wuaipinglab/sitePath documentation built on Sept. 26, 2022, 10:16 p.m.