[Bio-software] Advice about DNA alignment

Gilad Lehmann via bio-soft%40net.bio.net (by giladle from bgu.ac.il)
Tue Jan 8 07:08:37 EST 2008

Hello everybody, I need an advice.

I want to align 30 homolog non-coding sequencess of  about 1800bp length with low similarity. In addition to substitutions and gaps, these sequences contain short and long tandem repeats in several non-identical locations. 

Which software is optimal for such an alignment? is it clustlW? T-coffee? maybe other software?
I would like to avoid using repeatmasker if possible so the software has to ignore the disrupting repeats.

Thanks in advance,

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