First version of the generic Gene-Tree Runnable
First runnable for Notung
Notung can derive from GenericRunnable
Notung is part of the default pipeline
GeneTree::species_tree() can return the non-default tree
The root_id of the new species-tree is dataflown on branch 2
New parameter to name the CAFE tree
Treebest first tries to use the "treebest" tree
hc_tree_structure can only be fired after notung
Different organization of the treebest/notung stage
Notung requires a binary tree
We need left/right_index in the CAFE tree
The setters accept undef values
First clear the gdb<->stn association hash before setting up the new values
The "treebest" tree is called "default" (again)
The binary tree can only be prepared after the default tree
TreeBest operates on the cDNA alignment: the coordinates have to be divided by 3
New option to dump the filtered alignment
New option in the GenericRunnable to use TreeBest/sdi
Should complain if the tag is missing