# sitePath: an R package for detection of site fixation in molecular evolution
## Getting help
Post on Bioconductor [support site](https://support.bioconductor.org/)
if having trouble using `sitePath`. Or open an
[issue](https://github.com/wuaipinglab/sitePath/issues/new?assignees=&labels=&template=bug_report.md&title=)
if a bug is found.
## Installation
[R programming language](https://cran.r-project.org/) \>= 4.0 is
required to use `sitePath`.
The stable release is available on
[Bioconductor](https://bioconductor.org/packages/release/bioc/html/sitePath.html).
``` r
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("sitePath")
```
The installation from [GitHub](https://github.com/wuaipinglab/sitePath/)
is in experimental stage but gives the newest feature:
``` r
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.
``` r
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.
``` r
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
