LowMACA relies on three external resources to work properly.
	-	Clustal Omega version 1.2.x, our trusted aligner (http://www.clustal.org/omega/)
	-	Ghostscript, a postscript interpreter needed to draw logo plots (http://www.ghostscript.com/)
	-	Protter, a tool for visualization of proteoforms and annotation of predicted sequences (http://wlab.ethz.ch/protter/start/)
Clustal Omega is a fast aligner that you can download from the link above. Be sure to have clustalo within your PATH. 
For Linux and MacOSX users don't forget to run chmod u+x clustalo.
If you don't want to install a local clustalo, you can use the clustal omega web service, 
but you will need perl with the modules XML::Simple and LWP. They are generally included in every new perl installation.

Ghostscript is an interpreter of postscript language and that is used by the R library grImport to draw logo plots. It is generally already present in most Unix OS.
	-	For Linux users, simply download the program from http://ghostscript.com/download/gsdnld.html and compile it
	-	For MacOS users there is a dmg installer at http://pages.uoregon.edu/koch/
	-	For Windows users, download the program from http://ghostscript.com/download/gsdnld.html and then you have 3 options:
		1. Put C:/Program Files/gs/gs9.05/bin in your PATH once for all (Adjust the path to match your gs installation)
		2. Run the command below at every new session of R
			# Needed only on Windows - run once per R session
			# Adjust the path to match your installation of Ghostscript
			> Sys.setenv(R_GSCMD = '"C:/Program Files/gs/gs9.05/bin/gswin32c.exe"')
		3. Put the command showed above in your .Renviron file

Protter is a cool predictor and visualizer of protein sequence secondary structures. It's a web-based tool and doesn't require any special setting except from a internet connection.