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.
Fix the warning message in case of missing dnafrag
New "timeout" parameter in RunCommand
Removed the hopefully last references to the member table
Merge pull request #2 from jherrero/master

Small changes in the modules for the AncestralAlleles for 1-bp indels
Cosmetic changes suggested by podchecker
Merge remote-tracking branch 'github/release/75'

* github/release/75:
  Fix the warning message in case of missing dnafrag
Suggestion to add an alias for this species
The core databases are now in v76
We loop on TrimAl as long as it removes members
Updated the minimum requirement for eHive
Things are simpler if TrimAl updates the "gene_count" tag
More debug information
We can also store the "division" tag for HMM clusters
New option to load a file of HMM annotations (e.g. best-fit models)
JTT is the default model
Merge remote-tracking branch 'github/release/75'

* github/release/75:
  Updated the minimum requirement for eHive
More adaptors use bind_param()
dnafrag_id must be defined to get other chr prop

Otherwise, the base Locus object would "fail fetching the data from other
sources"