seq_reformat: added +pdb2contacts and +seq2contacts to produce contact lib for RNA and Protein structure based evaluation; seq_reformst: added the contact as an evaluation mode for the +evaluate option; seq_reformat: added the maintenance of AA case information when threading DNA onto a protein MSA (+thread_dna_on_prot_aln);seq_reformat: added the possibility to thread dna onto proteins when requesting tcs output