phylotools is an R package to assist you in building supermatrix using aligned fasta/phylip files. To install it, please use the following command in R:

library(devtools)
install_github("helixcn/phylotools", build_vignettes = TRUE)

If you haven't had devtools installed, you can install it by typing "install.packages("devtools")" in the R console.

Please feel free to send an email to the package maintainer Dr. Jinlong Zhang if you have any question or comments about this package.