This section details a number of additional packages and programs useful for working with structure (VMD), sequence (Seaview) and text/code (ESS). A brief description of how to obtain additional R packages is also included.
Recommended additional R packages include filehash, bigmemory and ncdf. These can be most easily installed from within R with the command:
install.packages(c("filehash", "bigmemory", "ncdf"), dependencies=TRUE)
Alternatively to install a source package on your system type at the command line:
R CMD INSTALL /path/to/pkg_version.tar.gz
There are lots more packages that contain functions to extend the capabilities of R. Most of these can be found on CRAN (Comprehensive R Archive Network) which is a network of ftp and web servers around the world that store identical, up-to-date, versions of code and documentation for R. From CRAN you can obtain gzipped tar files named pkg_version.tar.gz, which may in fact be “bundles” containing more than one package. Packages of particular note to the bioinformatics community include Seqinr and Bioconductor.
Muscle is a fast multiple sequence alignment program available from the muscle home page. The bio3d 'seqaln()' function currently calls the 'MUSCLE' program, hence MUSCLE MUST BE INSTALLED on your system and in the search path for executables.
A note for Mac users from Valeriya Simeonova:
After downloading MUSCLE, it should be unzipped and renamed just to "muscle" and placed in a directory such as "/usr/sbin/"
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics. Visit the VMD website for download information and documentation.
Along with the standard documentation you may find my VMD cheat sheet useful. I have also included a link to my .vmdrc file which includes a number of timesaving customizations (see the cheat sheet for full details).
Stride is a secondary structure analysis program available from the EMBL-Heidelberg. Stride is similar in functionality to the more prevalent dssp (see below). However, stride is much easer to setup as you may be able to simply copy or link to the stride executable distributed within every version of VMD (see above).
Dssp is another secondary structure analysis program available from ... look on google.
Again this should be installed on your system as an executable called "dssp" and be in the search path for executables.
Seaview is a graphical multiple sequence alignment editor. Download information and documentation are available here. I use Seaview to manually check and edit protein sequence alignment files pior to detailed analysis. I believe this should be done with every alignment regardless of how accurate the various automatic tools are supposed to be.
Emacs Speaks Statistics (or ESS) is an add-on package for Emacs to allow the easy editting of R scripts. ESS provides a standard interface between a range of statistical programs and statistical processes. It is intended to provide assistance for interactive statistical programming and data analysis, and is based on and extends the capabilities of S-mode. The code is freely available but is not in the public domain. It is distributed under the GNU GPL from here.