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Phylogeny-based sequence clustering with site polymorphism

Bioconductor version: Release (3.19)

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.

Author: Chengyang Ji [aut, cre, cph] , Hangyu Zhou [ths], Aiping Wu [ths]

Maintainer: Chengyang Ji <chengyang.ji12 at>

Citation (from within R, enter citation("sitePath")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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An introduction to sitePath HTML R Script
Reference Manual PDF


biocViews Alignment, MultipleSequenceAlignment, Phylogenetics, SNP, Software
Version 1.20.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License MIT + file LICENSE
Depends R (>= 4.1)
Imports RColorBrewer, Rcpp, ape, aplot, ggplot2, ggrepel, ggtree, graphics, grDevices, gridExtra, methods, parallel, seqinr, stats, tidytree, utils
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Source Package sitePath_1.20.0.tar.gz
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