DNA Multiple Sequence Alignment

[Janine Graves]

I'm a mathematician just starting to look at multiple sequence alignment
of DNA.  I'm not very familiar with the field and seek references on
algorithms or survey articles on this subject.

We have many thousands of sequences that must be aligned. They include
quality factors for each base call.  Speed is important.  We are also
looking for an algorithm that will find and flag chimeras among these
sequences.

Thanks,
  Janine Graves