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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.
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BioEdit's
features
include:
New version is WinXP
compatible
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· Several modes of hand alignment
· Automated ClustalW alignment
· Automated Blast searches (local and WWW)
· Plasmid drawing and annotation
· Accessory application configuration
· Restriction mapping
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· 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
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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longer being reliably maintained, and the documentation is out of date and no
longer maintained.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.
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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?
Are you willing to spend a little bit of time trying a
program without a complete help file or tutorial?
Can you tolerate free software that is unfinished and may contain an
occasional bug?
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)
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
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