These are little mini reviews of software that you may find interesting. I hope to add to these over the coming months.
Sequencing improvement software
These programs improve the quality of you DNA sequencing traces or provide you with an feedback on any problems found in your traces.
PeakTrace DNA basecaller - A new DNA sequencing basecaller for the ABI sequencers which gives increases in read length of 15 - 100%. It works with the ABI 377, 310, 3100, 3730, 3130 and 3730 sequencers.
There is a free web version of PeakTrace avaible too.
QualTrace - A unique command line program that examines the raw trace data to determine what is the limiting factor in trace read length. It is very helpful for identifying problems and also for optimizing your sequencing protocols. There is also a free online version of QualTrace that you can trial with your own trace (Windows/Linux).
Auto QualTrace - A graphical version of the QualTrace program designed to be easier to use by small users (Windows)
LongTrace - An interesting service which reprocesses your ABI trace files to extract more high quality bases from the blurry ends of your trace files. A free trial version is offered to test it on your own traces (Windows/Mac/Linux)
CounterTrace - A similar system to LongTrace but this uses a stand alone software package along with a special standard that is added to the sequencing reaction after clean-up. CounterTrace is designed to be used with phred base caller and works with both the ABI 3700 and 3730 instruments.
Trace viewers
These programs allow you to view your trace files. Some allow you to edit the sequence too.
Sequence Analysis - This is the software supplied by ABI. It is complex and very expensive (Windows 2000/XP only).
Chromas - A commerical windows traces viewer.
FinchTV - A free cross platform program for viewing traces files. Also allows you to view the raw signal data which is very useful for diagnosing sequencing failures (MAC/Windows).
4peaks - A free program for viewing ABI trace files. You can BLAST your sequences which is nice, but unfortunately you cant view the raw signal data (Mac OS X only).
DNA sequence assembly software
DNA Baser - A relatively low cost (US$495) commercial sequence assembler (Windows).
Phrap/Consed - Free for academic users, rather expensive for commercial users (~US$10,000). Large learning curve but very powerful (Window/Linux).
Staden - Open source assembly package. Very powerful but also has a large learning curve (Windows/Mac/Linux).
Sequencer - A commercial program that is quite expensive. I used to use this quite abit in the past buy now I just use Staden (Mac/Windows).
DNA annotation software
Software to help you analyze and annotate your sequences.
Artemis - Open source java application developed by the Sanger Center (Mac/Windows/Linux).
Primer selection software
Oligo - One of my personal favorites. It is expensive though (last time I checked it was over $1000)(Mac).