ANDES is composed of a set of Perl and R scripts.† For aligning profiles, ANDES depends on clustalw2.†
There is an excellent chance that your release of Unix already has Perl installed.† You can confirm this by typing the following at the command line:
You should see a result that tells you the exact path of the perl binary that will be executed by default, for example:
If you get something like:
perl: Command not found.
Then you will need to either download perl yourself, or ask your system administrator for help. Since this will be uncommon problem, we will not spend more time on this.
Currently, ANDES also uses the package Math::CDF.†
To install, please follow the instructions that are included.† If you can, try to have the system administrator install it in a central location so you will not have to deal with PERL5LIB paths, and the like.
It is more likely that you do not have R installed.† Fortunately, R is a very popular and well-maintained statistical software package which is very easy to install.† To download R, go to the R website:
It is easy to find the download link on their page; however, to initiate the download, you will need to select the CRAN (Comprehensive R Archive Network) mirror that is closest to you.
After installation, if your shell is able to detect where Rscript is installed when your invoke the following:
††††††††††† which Rscript
Then you should already to go.† If your shell canít find it, you may need to include the location of the Rscript binary in your PATH environmental variable.† How to do this will vary depending on your shell.
It is also likely you may not have clustalw2 installed.† You can download a copy from EBI at:
Follow the installation instructions that they have provided.† Chances are you just need to uncompress the tar.gz file that you download and then make sure your PATH environmental variable is pointed to where you uncompressed the tar file.† Again you can test to see if your shell can find clustalw2 by using the following command:
††††††††††† which clustalw2
To install ANDES, first go to our project download page, for the latest version.† You can find this at:
Move the archive to the directory you want to install ANDES, and then in that directory, run the following command to uncompress and explode the archive.
††††††††††† tar -xvf ANDES_<release date>.tgz
The <release date> should contain the date we uploaded the ANDES package, for example, 20091120.† When you execute the tar command, the ANDES directory will be created and all the Perl and R scripts, along with some sample data will be created.†