New parameters to set the location of the ortheus executable, the method_link_type and species_set_name of the alignment.
Also, parameters like the flank size and max. alignment length are set to their default values if not set by the user/pipeline.

There is a new parameter called "example" that sets most of the values such that it is easier for anyone to test to the code
with a toy region.
Changes in the modules to infer the AncestralAlleles for 1-bp indels

New parameters to set the location of the ortheus executable, the method_link_type and species_set_name of the alignment.

Also, parameters like the flank size and max. alignment length are set to their default values if not set by the user/pipeline.

There is a new parameter called "example" that sets most of the values such that it is easier for anyone to test to the code
with a toy region.

Slightly modified the output in the indel_X_XXXXXX_XXXXX file to report the final call.
Update MLSSIDFactory.pm

Runs dNdS for homoeologues as well
changed order of deletes - needed due to foreign key constraints to delete
7sauropsids branch lengths with Monodelphis as out-group
10 fish with mouse as out-group
Insert the missing dnafrags
Do not drop the tables (to be safe)
Merge pull request #8 from danstaines/master

OK !
Compara is eHive 2.0 ready !
change to file name to prevent use of brackets
hive_capacity=-1 is the default and should be skipped
Gene members should be removed from the families
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