README.md

In sitePath: Detection of site fixation in molecular evolution

sitePath: an R package for detection of site fixation in molecular evolution

Getting help

Post on Bioconductor support site if having trouble using sitePath. Or open an issue if a bug is found.

Installation

R programming language >= 4.0 is required to use sitePath.

The stable release is available on Bioconductor.

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("sitePath")

The installation from GitHub is in experimental stage but gives the newest feature:

if (!requireNamespace("remotes", quietly = TRUE))
    install.packages("remotes")

remotes::install_github("wuaipinglab/sitePath")

QuickStart

Both the phylogenetic tree and the matching multiple sequence alignment files are required.

library(sitePath)

# The file names of your tree and multiple sequence alignment
tree_file <- system.file("extdata", "ZIKV.newick", package = "sitePath")
alignment_file <- system.file("extdata", "ZIKV.fasta", package = "sitePath")

tree <- read.tree(tree_file)
tree <- addMSA(tree, alignment_file, "fasta")

Use the lineagePath function to resolve major lineages (the choice of threshold really depends). Then use the fixationSites function to detect fixation sites.

paths <- lineagePath(tree)

fixations <- fixationSites(paths)
print(fixations)

## This is a 'fixationSites' object.
## 
## Result for 4 paths:
## 
## 109 139 894 2074 2086 2634 3045 3144 988 1143 2842 3328 3398 107 1118 3353 
## No reference sequence specified. Using alignment numbering

sitePath documentation built on April 17, 2021, 6:05 p.m.