[BiO BB] Orthologous upstream sequence analysis

[Samantha Fox]

Hii...
I am looking for various options to analyze a set of 300bp long orthologous
sequences from a group of phylogenetically related species. Its like 5-8
promoter dna sequences per gene for around 2000 genes.

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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