The AMOVA functions make reference to specific entities such as locus. 
From glancing through AMOVA documentation, should not the variable names be generic, ie "species"?

See the style guide. Using '.' has meaning in computer science is best avoided for variable and function names.

New program organization. Notice /src, /doc, /testenv

Have refactored version of full_analysis.
Perhaps rename the script something that emphasises the purpose, loci, etc
The comments I removed may be needed if they are specific to the particular task, 
rather than AMOVA functions

Installing arlecore... success?? Need to look over the output. Was a bit odd.. might need to submit a patch.