Minor change
Swtiched to 10 maxtrys
Restructured alignment stage

— I made changes to the way aligner works
— Now trys are worked out by aligner and not in the stage script
— this makes the stage script a bit simpler
Outgroup optional

— Outgroup is determined by whether there is a species called out group
in the alignment
— If there is not, the most distally related species is selected
Big rearrangement

— firstly I fixed BLAST by changing it to blastn and correcting the
positions returned
— then I restructured the way the aligner.run works by creating
separate seed and add functions, this way i separate the counting of
trys and the actual alignment processes
Add outgroup to taxon tree
New functions

— added new functions to make out group optional
— getOutgroup
— getConstraintArg
New error class
Changes to tests to account for differences