Merge pull request #12 from nemami/master

Request 1/7
Subtree grafting switched to Phylo MRCA method (corrects length reoptimization). Added function sanitizeInputs.
Subtree grafting switched to Phylo MRCA method (corrects length reoptimization).
Added argument to enable nucleotide based branch length optimization (--oplnuc)
Support for nucleotide based branch length optimization (--oplnuc).