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,