[Bioperl-l] Re: Comparative genomics

[Elia Stupka]

> Is this a tree per gene ? How many species (nodes) per tree? If the trees are

Initially I was thinking of taking an EnsEMBL family to build the tree
from, but generating the families across multiple genomes, how does it
sound?

> essential, do not use the common NODE(ID, PARENT_ID, NAME) type schema: it's
> only efficient for getting the direct parents or children of a node. If
> that's not enough (e.g. you want complete subtrees or lineages etc.), use
> Celko's NODE(LFT, RGT, ID, NAME) schema. Or a hybrid of the two.

hmmm... think I need to talk to you about this one, I saw something with
nested brackets, where each bracket opening was a new level of depth in
the tree, are we talking about the same thing?

Elia

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