[Bioperl-l] Re: Comparative genomics

[Tony Cox]

On Fri, 28 Sep 2001, Elia Stupka wrote:

+>> 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?

I spent years in this area in a previous life......

There are several matrix formats. The one I used/prefer was #NEXUS format - used
by several of the best pylogenetic (ie cladistic) reconstruction programs like
Paup. It has the facility to embed a complete analysis configuration, data and
the output in nested tree descriptions.

see

http://paup.csit.fsu.edu/nfiles.html

Tony

******************************************************
Tony Cox			Email:avc@sanger.ac.uk
Sanger Centre	 		WWW:www.sanger.ac.uk
Wellcome Trust Genome Campus	Webmaster
Hinxton				Tel: +44 1223 834244
Cambs. CB10 1SA			Fax: +44 1223 494919
******************************************************