added creation of nestedset left/right indexing to process of loading and storing the trees.  Extended the meta tag system to include PHYML_alignment:(aa, cdna) and tree_method:(PHYML)
added creation of nestedset left/right indexing to process of loading
and storing the trees.  Extended the meta tag system to include
PHYML_alignment:(aa, cdna) and tree_method:(PHYML)

danstaines/ensembl-compara,kumarsaurabh20/ensembl-compara,danstaines/ensembl-compara,Ensembl/ensembl-compara,dbolser-ebi/ensembl-compara,kumarsaurabh20/ensembl-compara,dbolser-ebi/ensembl-compara,Ensembl/ensembl-compara,kumarsaurabh20/ensembl-compara,Ensembl/ensembl-compara,etapanari/ensembl-compara,Ensembl/ensembl-compara,danstaines/ensembl-compara,dbolser-ebi/ensembl-compara,Ensembl/ensembl-compara,danstaines/ensembl-compara,ckongEbi/ensembl-compara,danstaines/ensembl-compara,ckongEbi/ensembl-compara,etapanari/ensembl-compara,Ensembl/ensembl-compara,Ensembl/ensembl-compara,Ensembl/ensembl-compara,ckongEbi/ensembl-compara,etapanari/ensembl-compara,etapanari/ensembl-compara,kumarsaurabh20/ensembl-compara