Ensembl/ensembl-compara — pull request #1 by jherrero (2014-02-11 15:12:53+00:00)
Title: 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.