phylostratr

Predict and explore the age of genes using phylostratigraphic methods.

Installation

You can install from GitHub with:

library(devtools)
install_github("arendsee/phylostratr")

Dependencies

• R packages from CRAN (see DESCRIPTION)
• Biostrings from Bioconductor, install with devtools::install_bioc("Biostrings")
• NCBI BLAST+ - blastp (the protein BLAST command) must be in PATH. You can tell if blastp is properly installed by calling blastp -help from the command line.

Citation

Zebulun Arendsee, Jing Li, Urminder Singh, Arun Seetharam, Karin Dorman,
Eve Syrkin Wurtele (2019) "phylostratr: A framework for phylostratigraphy." Bioinformatics. https://doi.org/10.1093/bioinformatics/btz171

Funding

This work is funded by the National Science Foundation grant:

NSF-IOS 1546858 Orphan Genes: An Untapped Genetic Reservoir of Novel Traits