In article <1eb3f133.0401310536.3777b7c9 at posting.google.com>,
Andrea <webmaster at bioinformatik.de> wrote:
>I am looking for an algorithm which helps to identify possible SNPs in
>a multiple alignment of sequences.
>Do I need to have the trace file information for this?
You could probably make educated guesses without the trace data, but the
trace data definitely helps. In a previous job we used polyphred to do
this. This uses some extra data files output by phred to annotate SNPs
on phrap assemblies. It was rather good at identifying heterozygotes,
less good at homozygotes.
Mind you - I'm talking about 3-4 years ago, and I'm sure more has been
done in the field since then.