[Bioperl-l] Re: Comparative genomics

[Elia Stupka]

Dear David,

Thanks for the useful input, it is imporant to know what annotation will
be associated with each node of the tree. Do you think the annotation will
always be associated to each individual node, or should we allow for both
whole-tree annotation and individual node annotation?

> All of these can be accommodated in the nested parenthesis notation,
> but for large families or large collections of trees, the strings may
> get quite large.

Oh, by all means, we are not going to store these as strings, I was
referring to the strings as the format I had seen that we will need to
parse. These will be parsed into full relational db tables, and objects.

> In addition, it would be worth allowing for a description of the method 
> used to generate the tree(s).

What started my post was the fact that we will be trying to integrate this
in the standard Ensembl pipeline, so in that case the tree building would
have an analysis table and object associated with it, which would specify
how the results were obtained.

Elia

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