Initial integration of alnclst iterative HM eval
Added argument groups for ease of browsing options
Merged argument grouping into clustering branch; fixed conflicts
Added argument groups descriptions and cleaned up help strings
Comment correction
Added small cluster merging to analyze
Set up writing out of final alnst; clustering now has it's own write method
Added alnclst example to cli_test
Added cli test for splitting an alignment given an empty sites file
Merge branch 'clustering' into betarat-refactor
Factored out alnclst
Merge pull request #18 from fhcrc/17-alncst-factor

17 alncst factor