Alternative software for Geneious - expired software... (Oct/12/2010 )

Dear All,
I am looking for software, preferably freeware for my bioinformatics work.
Briefly, my work begin after DNA sequencing where I align the forward and reverse sequenced together based on the chromatogram and perform manual alignment when there is any ambiguous. Finally I will export the consensus (based on the quality of chromatogram) for further work.

Geneious works pretty easy for me to work but however my trial version is getting expired. I was wondering if there are any program which could work the same way.
I tried CLC sequence viewer but however it doesn't shows the quality of the chromatogram. I heard about NTI vector but is not free.

Any suggestions?

Thanks.

Adrian

you can try codoncode aligner.

Thanks mdfenko, now I'm downloading it and try out...

Anyone uses any other "free" program?

CodonCode Aligner does exactly what you need to do. Unfortunately it is not free. If you familiar with Unix, there is a software combiner, Phred, Phrap, and Consed. They do exactly what CondonCode Aligner does in window system.

there's also the staden package.

Hmn... staden package is interesting, but then no choice but I have to learn and install unix system...

Anyone knows ss there any shortcut or tutorial to make it (staden etc) usable in windows?

Thanks.

the latest windows installer version of the staden package is 1.7.0.

the author will eventually prepare an windows installer for the latest version.

Hi mdfenko.
Thanks for your reply.
I just got the link and is now downloading the software.

Cheers
Adrian