===============================================================================
2.1.0 

   This is a major new release. Please see the paper Havgaard et al. 2007 for
   details.
   
   Major undocumented changes in the usage of the algortihm.
   
   1: The -max_diff parameters now defaults to 25.
   
   2: During global alignment an attempt to align two sequences with a length
   difference larger than -max_diff will be aligned using a -max_diff equal to
   1.1 * the length difference.
   
   3: During global alignment the algorithm uses the global alignment score
   matrix if no other score matrix has been specified.
   
   4: The program can read sequences from STDIN. Running foldalign without any
   files will therefore not print the help text any more (use option -help).

   5: In addition to the changes described in the paper two of the default
   energy parameters have been changed. The cost of closing a multibranched
   loop has been raised from -34 to 0 to compensate for the missing dangling
   ends. The cost of extending an unpaired nucleotide in external/multibranched
   context is changed from 0 to -1. This should make it harder for these loops
   to grow unchecked.
   
   6: The Z-score printed by the locateHits script is calculated from the
   non-overlapping alignments, not from all the LS scores.
