2013-05-20: PETcofold v3.1.4 -> PETcofold v3.2
 * PETcofold comes together with PETfold v2.0 as C version using
   Vienna RNA Package library and Pfold library
 * PET reliabilities are returned including gap-columns (parameter --ppfile) 
 * parameter --setdelta replaces -setpetcon
 * parameter --setgamma replaces -setpartprob
 * rename "Normalized Score" to "Score" (like in PETfold)
 * remove parameter -LP


2013-05-20: PETcofold v3.1.3 -> PETcofold v3.1.4
 * thermodynamic partial probability is calculated by sequence number
   normalized delta G's (before non-normalized)
 * calculate unpaired thermodynamic cofold-probabilities before
   adjustment by partprob (switch functions get_prob_unpaired_seq and
   multiply_partprob_paired; in older version unpaired thermodynamic
   cofold-probabilities were adjusted twice by partprob)
 * set RNA(co)fold option '--noLP' by default (same as in PETfold) and
   replace parameter -noLP by -LP
 * for RNAfold in function get_fasta_file, bases in gap-free sequences
   are only constrained as base paired when pairing partner isn't a gap 
 * solve stem extension bug where base pairs get constrained that
   aren't connected with the constrained stem
 * now also for SETSTRUC: merge intramolecular reliabilities for bases
   with large intramolecular basepaired reliabilities and
   intermolecular reliabilities for the other bases
 * delta (petcon) is set back for the second alignment


2013-05-20: PETfold v2.0pre -> PETfold v2.0
 * reads PPfold calculated reliabilities from STDIN (parameter --ppfold)
   to replace slow Pfold calculations for large alignments
 * check for valid alignment as input (sequences of same length)
 * PET reliabilities are returned including gap-columns (parameter --ppfile) 


2011-11-07: PETcofold v3.1.2 -> PETcofold v3.1.3
 * add parameter --setstruct for entire duplex structure which set
   partial structure bp-reliabilies to step1 bp-reliabilities
 * rename "Reliability" to "Normalized Score" (like in webserver)
 * don't break identifiers at 1st dot (like in webserver)
