[BiO BB] promoter sequence analysis for TFBS .. using phylogeny

[Samantha Fox]

 Hii...
I am looking for various options to analyze a set of few hundered bp long
orthologous sequences from a group of phylogenetically related species. Its
like 5-8 homologous promoter dna sequences per gene for around thousand
genes. The motivation is to get the conserved motifs which have remained
constant under selection.

What can be the best ways to do this analysis, I looked at some phylogenetic
tools, but most have limitations like web-based, just 2 sequences, etc.

All your suggestions... and anyone experienced with similar stuff. ... I
welcome it all...

Thanks.
 Samantha
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