Make a separate trebest analysis for small families (RAxML path)
Non-reachable analyses are now discarded from the graph
Fewer analyses in the tree-HC section
Switched back to HMMer v3

HMMer v2 cannot calibrate many CDS HMMs. We revert to HMMER v3 being the
default for both kinds of alignment, and we also use HMMER v2 on
amino-acide alignments in order to use pantherScore
Some more conditions are evaluated at init_pipeline time
New option to disable QuickTree-break
hc_tree_attributes can now be run right after treebest
We don't need ortho_tree_annot any more (and homology_entry_point)
We can skip "finalize_entry_point"
Ensembl does not use QTB
Treebest is split into smaller analyses
"failed_job_tolerance" is not considered in semaphore blocks
New Runnable to dataflow based on several conditions on a gene tree
Merge branch 'master' of github.com:Ensembl/ensembl-compara

* 'master' of github.com:Ensembl/ensembl-compara:
  minor changes for 78
  minor changes
  minor changes
  Passing a GeneTree to dumpTree...
  print_alignment_to_file has to be called on the tree, not on the node
We can build an AlignedMemberSet on any node
Let's use the GeneTreeMultiConditionalDataFlow runnable
HCs should fail quickly
Colons are not allowed in eHive's parameter-substitution
clear() doesn't really reset the list of Members, just empties it
Tags must be read by the derived module