sitePath
Phylogeny-based sequence clustering with site polymorphism
Bioconductor version: 3.23 · Package version: 1.28.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("sitePath")Details
| Maintainer | Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn> |
| Author | Chengyang Ji [aut, cre, cph] (ORCID: <https://orcid.org/0000-0001-9258-5453>), Hangyu Zhou [ths], Aiping Wu [ths] |
| License | MIT + file LICENSE |
| URL | https://wuaipinglab.github.io/sitePath/ |
| Bug Reports | https://github.com/wuaipinglab/sitePath/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, MultipleSequenceAlignment, Phylogenetics, SNP, Software |
| Package Short Url | https://bioconductor.org/packages/sitePath/ |
Citation
From within R, enter citation("sitePath"):
Chengyang Ji. sitePath: Phylogeny-based sequence clustering with site polymorphism. doi:10.18129/B9.bioc.sitePath, R package version 1.28.0, https://bioconductor.org/packages/sitePath.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | sitePath_1.28.0.tar.gz |
| Windows binary (x86_64) | sitePath_1.28.0.zip |
| macOS binary (arm64) | sitePath_1.28.0.tgz |
| macOS binary (x86_64) | sitePath_1.28.0.tgz |