Freeware/Shareware for PC, Mac and Linux

A far from complete listing of freeware and shareware applications for 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 in the directory MolBio

A similar collection can be found at the European Bioinformatics Institute's ftp site

An excellent site for Linux scientific software is, the SAL site (look under the Chem/Biol. section)

Multiple alignments:

ClustalW and its graphic front-end, ClustalX, are free programs for Mac, PC and UNIX (which will run on Linux, or even from your home directory on watson.achs.virginia.edu) - they can also be obtained here (another site for native Mac OS X versions can be found here). 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 (both ver.1 and ver.2 as a beta release)

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 program (Java Runtime Environment, or JRE). Mac OS X users will have JRE installed. 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.

While the PAUP* and MacClade programs are commercial, they are reasonably priced and 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 uti lity, 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 allow for easy transfer, via the desktop clipboard, to your favorite drawing program (eg. PhotoShop, FreeHand, PowerPoint, etc).

Please email comments or suggestions about the ACHS MolBiol pages to mblack@virginia.edu.

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