BioEdit is a biological sequence alignment editor written for Windows 95/98/NT/2000/XP.  An intuitive multiple document interface with convenient features  makes alignment and manipulation  of sequences relatively easy on your desktop computer.    Several sequence manipulation and analysis options and links to external anaylsis programs facilitate a working environment which allows you to view and manipulate sequences with simple point-and-click operations.   BioEdit's features include:                      New version is WinXP compatible  Several modes of hand alignment Automated ClustalW alignment Automated Blast searches (local and WWW) Plasmid drawing and annotation Accessory application configuration Restriction mapping RNA comparative analysis tools Graphical matrix data viewing tools Shaded alignment figures Translation-based nucleic acid alignment ABI trace viewing, editing and printing Customizable ... other features Note: Although BioEdit was recently updated, it is no longer being reliably maintained, and the documentation is out of date and no longer maintained.  It is being updated slowly, but there is no guaranteed finish date.  Until documentation is complete, play with the menus and see what happens, or email with a question.

Note:  If you have trouble launching BioEdit on Windows NT, try replacing BioEdit.exe with this version

Sequence/contig assembly:
BioEdit does not directly do assemblies of sequencing data.
There is an assembly editor available called BioLign that might serve your needs if they fit a fairly narrow definition.  Please answer the questions below to determine if BioLign is worth trying for your needs:

Do you routinely sequence the same gene or highly related genes that are <10 Kb?
Do you need a way to align assemblies of homologous sequences that maintains a link to the trace data?
Do you have access to phred and phrap?

If so, would it be nice to:

• Have assemblies automatically oriented in the same direction and automatically aligned?
• Open all traces of an assembly aligned at a position by clicking the base in an alignment?
• Scroll traces of an assembly automatically while keeping them aligned at a particular screen position?
• Open and close traces automatically as an assembly scrolls through their ranges?
• Jump to assembly positions that are different from a consensus, a reference, or disagree in reads?
• Manually align assemblies (contigs) while maintaining the alignment of the traces in each assembly?
• Edit assemblies in both the alignment and contig view interfaces?

If the answer to these is yes, then feel free to download and try out BioLign.
There is an online help file with a general introduction to the basics of the program and its use.
There are several newer features that are not documented at this time, however.
If BioLign does not suit your needs, suggestions, bug reports and criticisms are always welcome.
If you find the program simply intolerable and annoying, please just delete it.

Click here to download the current BioLign installation (v 4.0.6)

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Current version 7.0.5 Last updated 5/31/05 Tom Hall thall@isisph.com

RNaseP database

ReadMe file

See screen shots

Accessory applications

Multi-file download

email Tom

Older BioEdit versions:
Note:  There have been some requests to go back to version 5.0.9.  If you would like to download the 5.0.9 installation, you can get it here.

Other versions:
Version 7.0.4
Version 7.0.3
Version 7.0.2
Version 7.0.1
Version 7.0.0