BioEdit is a multifunctional sequence alignment editor that runs under Windows 95/98/NT/2000/XP.

Features include:

• Intuitive user-friendly multiple-document GUI interface
• full-color with point-and-click color editing
• multiple modes of hand-alignment, including dynamic grab-and-drag on the screen
• full color single-sequence editing
• Graphical feature annotations
• Display and print ABI sequence chromatograms
• Shaded alignment outputs with many options, rich text export and metafile clipboard copy
• edit, manipulate and analyze protein and nucleic acid sequences
• run restriction maps
• draw and annotate plasmids
• RNA comparative analysis (Mutual information, covariation) with dynamic graphical matrix data viewer
• vertically- and horizontally-split window views
• read and write 5 standard formats (GenBank, Fasta, Phylip3 & 4, PIR) and import/export several more with D. Gilbert's ReadSeq
• Includes a binary file format for fast read and write of large files -- suitable for 20 Mb+ files
• Retain GenBank field info in GenBank or BioEdit files
• Configure accessory applications to automatically run through GUI interface -- automatically feed sequences to app and automatically open output file(s) in BioEdit or other apps
• Several accessories pre-configured and come with distribution, including ClustalW (D. Higgins, et al.) and some PHYLIP programs (J. Felsenstein)
• TreeView (R.D.M. Page) installation also comes with distribution
• Local BLAST accessories -- automatically create BLAST databases and run searches right on your computer -- also includes BLAST 3.0 client
• Retrieve sequences from GenBank
• on-line help -- this is quite out of date and there is no time to update it at this point.

If you are upgrading from a previous version of BioEdit, and you have accessory applications configured, make sure to back-up the "AccApp.ini" file in the BioEdit apps folder.  A full install will overwrite this file with the default configurations. 

Note:  An early bug that has been in all previous versions of BioEdit was fixed on 6/29/1999.  All previous versions have this bug, but it almost never surfaces. If you get a message saying "Error in startup routine", then "EAccessViolation", upgrading to the most recent version should fix this. 

Another note:  BioEdit is not a powerful sequence analysis program, especially in the realm of proteins and molecular structure.  Its main intent is a rich interface for sequence alignment, viewing and manipulation.  It does, however, offer a nice interface for comparative analysis of RNA secondary structure through mutual information with interactive graphical display of data. 

If you are interested in a very nice alignment editor with an emphasis on protein chemistry, structure, and phylogenetic relationships of sequences, I would direct you to GeneDoc.  You may still find BioEdit useful for many simple and quick manipulations, multi-format compatability, easy viewing of sequence info (gb or bio formats) and a few graphical gizmos. 

To find (free) software to fullfill needs not covered by either GeneDoc or BioEdt, you might try looking in the following places (as a start): 

The Weizmann Institute Software in Biology and Bioinformatics
The European Bioinformatics Institute searchable database for molecular biology software and resources
Software links at Taxonomy and Systematics at Glasgow
The EMBL BioCatalog
Software archive at IUBio

Or, for resources available on the WWW, you might try Pedro's BioMolecular Research Tools

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