BioEdit's features include:
New version is WinXP compatible
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.
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is out of date and no longer maintained.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.
Several modes of hand alignment
Automated ClustalW alignment
Automated Blast searches (local and WWW)
Plasmid drawing and annotation
Accessory application configuration
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
If you have trouble launching BioEdit on Windows NT, try replacing BioEdit.exe
with this version
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:
Are you willing to spend a little bit of time trying a program without
a complete help file or tutorial?
Have assemblies automatically oriented in the same direction and automatically
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
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?
Can you tolerate free software that is unfinished and may contain an
If the answer to these is yes, then feel free to download and try out
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,
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
Click here to download the current
BioLign installation (v 4.0.6)
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.