[ensembl-dev] documentation missing

Joe Carl joseph.w.carl.jr at gmail.com
Tue Feb 12 16:02:05 GMT 2013

I'm reading the compara database scheme webpage (
http://www.ensembl.org/info/docs/api/compara/compara_schema.html), and
noticed the three most intersting functions (to me) are missing.

where is the documentation for the following

   - species_tree_node<http://www.ensembl.org/info/docs/api/compara/compara_schema.html#species_tree_node>
   - species_tree_node_tag<http://www.ensembl.org/info/docs/api/compara/compara_schema.html#species_tree_node_tag>
   - species_tree_roo<http://www.ensembl.org/info/docs/api/compara/compara_schema.html#species_tree_root>

My goal is the following:

1) Grab the phylgentic trees already generated by ensemble (for specific
Gene ID)
     a) Newicks
     b) Sequences by species
2) Grab the DN/DS for various branch points from Pig to Human

If I need to I will grab the gene ID for each species and then determine
the proper nucleotide sequence and grab those, using the newick calculate
Dn/DS using PAML to get descendant predicted LCA sequences.

Is there a better way to do this than I have outlined?

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