[BiO BB] SNP analysis program

[Bossers, Alex]

We have been using Mutation Surveyor from Softgenetics for large scale
SNP detection (eukaryotic). Although commercial, it works great.
For large EST assemblies (depending on the source EST/genomic) we have
been using the package from TIGR called TGICL.

Good luck,

Alex


-----Oorspronkelijk bericht-----
Van: bio_bulletin_board-bounces+alex.bossers=wur.nl at bioinformatics.org
[mailto:bio_bulletin_board-bounces+alex.bossers=wur.nl at bioinformatics.or
g] Namens Hongyu Zhang
Verzonden: woensdag 14 februari 2007 22:22
Aan: bio_bulletin_board at bioinformatics.org
Onderwerp: [BiO BB] SNP analysis program

Dear all,

I am looking for a SNP analysis program, which is good at

Assemble 
chromats
Allow me to edit 
chromats

Displays mixed 
bases

Displays polymorphisms 
calls



We have looked at Polyphred and Sequencher. Polyphred works well in
Linux/Unix, so it can be wrapped in a shell script to run in batch mode
processing bulk data. It is also in good compatibility with Phred/Phrap
and consed. Sequencher has nice GUI and runs on Windows, which is good
for scientist to do annotation interactively, but I am not sure whether
it can be run in batch mode.

If you have any good suggestions, please let me know. Thanks!


 
Hongyu Zhang, Ph.D.
Computational biologist 
 Ceres Inc., Thousand Oaks, CA
Cell: 805-405-5394
Fax: 866-447-8750


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