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Welcome to the FAVE wiki!
Both FAVE-align and FAVE-extract are a collection of Python scripts. As such, you'll need to download and install Python before using them. The FAVE suite was developed in Python 2.x, so we recommend installing the most recent Python 2.x version (2.7.6 as of writing).
If you have any questions, or useful comments to make about FAVE, please post them to the FAVE users' group: https://groups.google.com/forum/#!forum/fave-users
FAVErtools R package
There is an R package called FAVErtools which mostly contains functions for reading Plotnik and FAVE files into R. To install in R:
library(devtools) install_github("FAVErtools", "JoFrhwld")
?FAVErtools or the FAVErtools README for more information.