bugfixes in get_4D_SimpleAlign()

- bugfix: the cdna alignment was not split in codons
- New option to only keep columns for which all the sequences code for the same 4D amino-acid
- New option to keep gaps
With -can_respecialize, we don't need to force analyses to be LOCAL
get_gene_tree_file() now needs a root node instead of the tree object
Introduced the concept of hidden genes to expand edits beyond split genes
Fixed RAxML_EPA_lb

Completely changed the runnable as:
 - long branches can split the tree in two halves, and we shouldn't remove
 any genes in this case
 - the EPA algorithm can (in some cases) create multifurcations. We now use
 the "binary tree constraint" mode (-r) to constraint the topology
New parameter to control the format of the input gene-tree file
For DNA, we always use the GTRGAMMA model
bugfix: #raxml_cores# not given to the raxml analyses
Use pthreads fo raxml_epa_longbranches_himem instead of -U
bugfix: should be HMMERv3 there
Disable HMMERv2 as it cannot calibrate some trees
Do not release tree tree there as we want to check its structure later
Fixed the paths to RAxML and Examl
bugfix: funny issues with the cache in get_all_Members
Merge branch 'release/77'

* release/77:
  bugfixes in get_4D_SimpleAlign()
minor: The "host" parameter is not needed here
Transformed some control-flow rules to semaphore blocks
LRGs are loaded in the master database