[Bioperl-l] Storing Sequences and Alignments

Aaron J. Mackey amackey at pcbi.upenn.edu
Fri Apr 2 08:33:17 EST 2004

I have an in-development (but currently in real-world use) database 
schema (CDAT) and accompanying software library (CDATlib) for storage 
and manipulation of phylogenetic "Character state Data And Trees".  
This includes storing multiple alignments (as a state matrix), as well 
as the underlying sequences, hierarchical sequence features and the 
trees that describe the phylogeny of members in the state matrix.  The 
interesting bit is that the state matrix may be probabilistic for 
inferred ancestral states, and may refer to features as well as 
sequences.  If this seems "up your alley", contact me for details.


On Apr 2, 2004, at 7:59 AM, michael watson (IAH-C) wrote:

> Hi
> I am after a database or schema that can store sequence and annotation 
> and also multiple sequence alignments.  I thought perhaps biosql might 
> do this, but I am not sure it does.
> Does anyone know of anything?
> Thanks
> Mick
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