text: -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
  -- Copyright [2016-2018] EMBL-European Bioinformatics Institute
  -- 
  -- Licensed under the Apache License, Version 2.0 (the "License");
  -- you may not use this file except in compliance with the License.
  -- You may obtain a copy of the License at
  -- 
  --      http://www.apache.org/licenses/LICENSE-2.0
  -- 
  -- Unless required by applicable law or agreed to in writing, software
  -- distributed under the License is distributed on an "AS IS" BASIS,
  -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  -- See the License for the specific language governing permissions and
  -- limitations under the License.
  
  # Updating the schema version:
  UPDATE meta SET meta_value = 61 where meta_key = "schema_version";
  
  # Add a new index to the "domain" table
  alter table domain add index method_link_species_set_id (method_link_species_set_id);
  
  # Add a new index to the "species_set" table
  alter table species_set add index genome_db_id (genome_db_id);
  
  # Add a new index to the "protein_tree_member"
  alter table protein_tree_member add index method_link_species_set_id (method_link_species_set_id);
  
  # Add a new index to the "protein_tree_member_score"
  alter table protein_tree_member_score add index method_link_species_set_id (method_link_species_set_id);
  
  # Add a new index to the "super_protein_tree_member"
  alter table super_protein_tree_member add index method_link_species_set_id (method_link_species_set_id);
  
  # Add a new index to the "nc_tree_member"
  alter table nc_tree_member add index method_link_species_set_id (method_link_species_set_id);
  
  # Modify tag column in table species_set_tag 
  alter table species_set_tag modify tag varchar(50) NOT NULL;
  
  