Google: "ribosomal database project" -- 97,000+ small and large subunit
ribosomal RNA genes (pre-aligned for your pleasure).

"Burnce"  wrote in message
news:ccknaf$msu$1{at}darwin.ediacara.org...
> Hello,
>
> I am working on a new algorithm for phylogenetic tree reconstruction. In
> order to validate my methods, I am looking for sequence alignments with
> the following characteristics:
> - hundreds to thousands of taxons
> - wide spread of taxons across phyla/kingdoms (not 100 species of
> squids...) - data from which a tree has already been calculated (and
> published) to
>   allow comparison of results
>
> What leaps to mind are cytochrome-C, Rbcl, ribosomal proteins.
>
> Does anyone have a dataset they can send me, or know where I might find
> such an alignment?
>
> Thanks,
>
> Burnce
>
>
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