[Nov 23, 2009 14:09] Web access to Microsoft Live@edu accounts now works.
Following is a far-from-complete listing of freeware and shareware applications of interest to molecular biologists.
General FTP sites with large collections of software
- Indiana University maintains a large collection of freeware, shareware, and demonstration software at their FTP site.
- A similar collection can be found at the European Bioinformatics Institute's ftp site.
Multiple Alignments
ClustalW and its graphic front-end, ClustalX, are free programs for Mac, PC, and UNIX/Linux.
- You can run the UNIX version from your home directory on watson.achs.virginia.edu.
- You can also get the programs from L'Universite de Strasbourg.
- Native Mac OS X versions are available at EMBL.
- ClustalW is also now included in the GCG suite of programs (ClustalW+).
Sequence Editors
- For the PC - BioEdit and GeneDoc are freely available.
- For the Mac - Se-AL is available
- SeqPup is another free sequence editor (still in developmental stage) available at Indiana University's software archive. SeqPup is a JAVA application, so users will also need to download and install a copy of the Java Runtime Environment (JRE). Mac OS X users will have JRE installed already. Windows and Linux users can download it from Sun's Java web site.
Phylogenetic Inference Programs
While PHYLIP is available, running under the GCG command line interface, anyone may download the program from the PHYLIP web site at the University of Washington. Dr. Felsenstein also maintains an extensive list of phylogenetic software (b oth free and commercial packages) available at other sites.
PAUP* and MacClade are commercial programs that are reasonably priced. Both are available from Sinauer publishing. GCG users should note that the Parsimony inference portion of the PAUP* package is available in GCG.
An extremely useful tool for people working with PHYLIP is Dr. Page's utility, TREEVIEW. This small program will read any NEXUS- or NEWICK-formatted tree (as well as other formats); can perform simple manipulations on the figure; and can allow for easy transfer, via the desktop clipboard, to your favorite drawing program (e.g., PhotoShop, FreeHand, PowerPoint, etc).