Fixed the accumulation of genome_db_ids for (non-)reused species
added a sub sub fetch_all_by_method_link_species_set_id_label_pattern
bugfix: no tags in Homology, just a direct access
Added check for the ss_cons bit
No warnings on missing mlss when looking for species_sets by name -- we may have more than one ss with the same name
Removed smartmatch
Added method to get a  Bio::EnsEMBL::Compara::GenomicAlignTree object either from a GenomicAlignTreeAdaptor, a SpeciesTreeAdaptor or from the species set. Removed smartmatch. Avoid getting masking for ancestral sequences.
Added method to get the original seqeuence (no insertions).
Added methods to use Bio::EnsEMBL::Compara::GenomicAlignTree objects. Added no_branch_lengths and compact_alignments parameters.
Updated deprecated call
Cleared erroneous cases of double-licensing
fetch_by_name_assembly() is throwing instead of returning undef, we need to wrap it in an eval{}
Revert "Moved away from Switch. Now using: feature qw(switch)"

This reverts commit 749c1136486cd3c6b9b564e01e899429da954bf0.

Conflicts:
	modules/Bio/EnsEMBL/Compara/Graph/NewickParser.pm
Cannot use given/when
Cache the SpeciesTreeNode objects to save queries
This way, we only redefine 1 method from Taggable
name is now an alias of node_name
modules to calculate branch lengths from multiple alignments
config to make new compara species tree with branch lengths estimated by phylofit
species_tree_node() may not be populated: we return undef in those cases