Update ProteinTrees_conf.pm

Added 'homoeologous_genome_dbs' for dealing with poplyploid genomes
Update EGProteinTrees_conf.pm

Added homoeologous_genome_dbs to deal with polyploid genomes
Update OrthoTree.pm

For homoeology pairs, don't only change the MLSS, but also the homology description.
Update EGProteinTrees_conf.pm

if division is plants, supersede the default 'taxlevels' parameter value.
Merge commit 'refs/pull/ensembl-github/12'

* commit 'refs/pull/ensembl-github/12':
  Update EGProteinTrees_conf.pm
  Update OrthoTree.pm
  Update EGProteinTrees_conf.pm
  Update ProteinTrees_conf.pm
Finalized the "homoeologous_genome_dbs" option

The files have been modified from the pull request:
 - homoeologous_genome_dbs is given to all ortho_tree* analysis
 - homoeologous_genome_dbs defaults to [] in the config files