README.md

GeneBridge: Rooting Orthologous Genes in Large-Scale Evolutionary Analysis.

GeneBridge is an R package that implements the Bridge algorithm to infer the evolutionary root of genes in a given species tree. By rooting orthologous genes in large-scale evolutionary snalysis, GeneBridge provides a framework for exploring the evolutionary roots of biological systems.

Installation in R (>=4.3)

Install dependencies to build the package's vignettes

install.packages("knitr")
install.packages("rmarkdown")

Install the GeneBridge package

install.packages("remotes")
remotes::install_github("sysbiolab/GeneBridge", build_vignettes=TRUE)

Examples

Follow the GeneBridge vignette and try to make some plots!

library(GeneBridge)
vignette("GeneBridge")

Citation

If you use GeneBridge, please cite:

• Campos et al. Bridge: A New Algorithm for Rooting Orthologous Genes in Large-Scale Evolutionary Analyses. Molecular Biology and Evolution 41(2):msae019, 2024. https://doi.org/10.1093/molbev/msae019

Licenses

The GeneBridge package is distributed under Artistic-2.0