New features and bug fix

New features

1. added the --u parameter to allow user-specified mutation rate #271
2. allow users to use the count_base.pl genome stats to replace the -genome_size and -seq_count parameters in util/buildSummary.pl.

Bug fix and enhancements

1. check RepeatMasker results in immediate steps to accommodate for situations when no repeat is found.
2. add more alias to the Sequence Ontology list and partially solve #151 and #178.
3. resolve the Illegal division by zero error when flanking sequences of candidate TEs are all N/X. #259