##-----------------------------##
Version 1.1
##-----------------------------##

Done:
- in functions.py changed def create_sorted_endpointlist(intervals) to make it faster
- changed mwis.py

- added pk_tools

Effect:
- speed-up

- show the best near-optimal pseudoknots

##-----------------------------##
Version 1.2
##-----------------------------##

Done:
- kissing hairpins
- global structure

Effect:
- prediction of kissing hairpins

- show the best near-optimal pseudoknots and kissing hairpins

- show the predicted global structure

Bugfixes:
- allowed overlap of 1nt at junction for pseudoknots with interrupted stems (pk_construction.py)

##-----------------------------##
Version 1.2.1
##-----------------------------##

Done:
- takes FASTA file with multiple sequences as input

##-----------------------------##
Version 1.3
##-----------------------------##

Done:
- implemented dynamic programming algorithm to speed up recursive secondary 
  structure element search for pseudoknot/kissing hairpin candidates
- general cleaning up

##-----------------------------##
Version 1.3.1
##-----------------------------##

Done:
- deleted redundant file bulges_internal.py
- drop thresholds in CC06, CC09, LongPK. These forced core H-type pseudoknot to have lower 
free energy than single hairpins (S1 and S2). However, it is preferable to have these 
thresholds AFTER recursive secondary structure elements in the loops are taken into account.
- assign (hopefully) unique file name to each sequence to allow DotKnot to run in parallel
for a set of sequences. After DotKnot is finished, files are deleted. File names start with an
(hopefully) unique identifier, which consists of the first 12 characters of the identifier 
given in the first line of the FASTA file.
- fix bug where overlapping brackets are printed incorrectly in pk_tools.add_recursive_elements()
- output CT file for global structure


