Added capellini.py and functions to create consensus newick file
In XMLBuildReader: creating and returning MultipleSequenceAlignment object instead of just consensus; In XMLBuildWriter: added composite and additional composite and consensus data
Changed consensus & domain variable names and calls to generate them
Changed get_hypergeometric_prob to get_hypergeometric_pval
preconsensus->composite; added get_pwm; added msa iterate capability
added PositionWeightedMatcher; var name changes; score matrix save changes
Added capellini params
updated domain clustering
Added MultipleSequenceAlignment class; added node type and matrix defaults
Updated composite and consensus calls
consensus->composite