Update EGProteinTrees_conf.pm

Updated the ktreedist resource class for Plants
Added methods get_all_sorted_GenomicAligns, original_sequence and cigar_line and some simple tests
Removed debug print statement
Set the species_order for PECAN alignments
Need to check if the tree has been restricted when trying to assign the reference_genomic_align when calling fetch_by_GenomicAlignBlock
Added sort_children function. Decided not to overwrite the inherited sorted_children function
Set the reference_genomic_align_node when creating a Bio::EnsEMBL::Compara::GenomicAlignTree object
Merge branch 'master' of https://github.com/Ensembl/ensembl-compara
Change scores with a value of 0 to 1 for display purposes
It is straightforward to use Bio::EnsEMBL::Storable in those objects
Member and MemberSet should also inherit from Storable
Production objects can also inherit from Storable
PeptideAlignFeature can also inherit from Storable
Graph::Node should not know anything about adaptors and storage
Many objects in Compara could / should be Storable
Removed the deprecated arguments of lignedMemberSet::get_SimpleAlign()
Homology has been cleaned-up
Removed NestedSet::newick_simple_format()
Removed GeneTreeNode::taxon_id()
Removed GeneTreeNode::taxon()