DumpTrees_conf is compatible with coreless Hive
typo
This file is in public-plugins/ensembl/htdocs/info/genome/compara/compara_stable_id_mapping.svg
the Makefile is not used any more
Updated doc based on latest Eleanor's comments
This SQL should have been updated a long time ago
New health-check for the guide species tree
Revert "DumpTrees_conf is compatible with coreless Hive"

This reverts commit 025745d959a74223d7e56dfbe9ed46636ea603e0.
The commit made the pipeline not compatible with the current stable
version of ensembl-hive
removed AlignedMemberSet::read_clustalw()
Removed AlignedMemberSet::load_cigars_from_fasta()
Added deadline for the deprecated arguments of AlignedMemberSet::get_SimpleAlign()
Correct way of dealing with homologies
Added deadline warning for NestedSet::newick_simple_format()
Removed deprecated calls to GeneTreeNode::taxon_id()
Species-tree leaves should be found by genome_db_id
Added deprecation deadlines
Removed deprecated calls to NestedSet::newick_simple_format()
It was never the case in >10 years, and it is not planned
Removed HomologyAdaptor::fetch_all_by_Member_method_link_type()
No need to import deprecate()