New healtcheck to ensure we have loaded the LRGs
Don't die if the "removed_columns" tag is missing
The reference tree may not be the default one

In that case, ref_root_id should not be the tree's dbID, but its
ref_root_id
Updated the capacities on the EBI farm
Propagate the "removed_columns" tag to other trees

The "removed_columns" tag is only stored in the default tree, but some
runnables may need it and use a non-default tree as input.
This commit propagates the tag in those cases.
New analysis to infer branch lengths with RAxML

Notung completely erases the branch lengths, and we need to run RAxML in a
special mode to infer the branch lengths, whilst preserving the topology
First version of long-branches recomputation
New Runnable to copy a tree between clustersets
New "copy_tree" analysis when RAxML cannot be run (< 4 genes)
cosmetic: fixed doc
Up-to-date dataflows
bugfix: runtime_tree_tag can exist and be undefined
docfix
New option to choose the alignment format

By default, it is still FASTA
bugfix: cdna coordinates and removed_columns

Coordinates should be divided by 3 before being put into a string
bugfix: Use $self->o() for homoeologous_genome_dbs
Depends on the Ensembl API v76
pipeline not compatible with eHive 2.1
The alignment length is also stored as a tag
Reorganized the alignment-filtering step

We now use Noisy as the standard filter (it removes fewer data, which
allows RAxML to infer better -longer- branch lengths).
This is coupled with a filtering decision step: we only run Noisy for the
large alignments, and prefer using the full alignment when it is small
enough.