2013-05-16 Release 1.1.1

	  --cluster-size=<n>        soft maximum of sequences in sub-clusters
	  --clustering-out=<file>   Clustering output file
	  --residuenumber, --resno  in Clustal format print residue numbers (default no)
	  --wrap=<n>                number of residues before line-wrap in output
	  --output-order={input-order,tree-order} MSA output order like in input/guide-tree

	turned off Kimura correction for DNA/RNA

	enable distance matrix output after initial mBed but subsequent full distance calculation

	enable termination after distance/guide-tree calculation (--max-hmm-iterations=-1)

	longer sequence labels 

2012-04-25 Release 1.1.0

   DNA and RNA support now added. Sequence type can be specified manually
   using --seqtype={Protein|DNA|RNA}

2012-03-27 Release 1.0.4

   zipped input now supported

2011-09-07 Release 1.0.3 

Bugs fixed:

   input failed if first line in fasta file was empty

   input failed if Clustal formatted file had trailing residue numbers

   '*' character was causing problems, did not get filtered out by squid 

   --outfmt=fasta was not recognized

   '~' gap characters were not recognized in MSF format

   amended README re sequence/profile alignment

   disallowed empty sequences

   doxygen documentation fixes and fix of API example

2011-06-23 Release 1.0.2

2011-06-17 Release 1.0.0 (DeshilHollesEamus)

2010-06-17 Release 0.0.1 (Dubliniensis)
		
		First "release" as program has been able for a while to perform
		all basic tasks without problems.

		Non-standard features already built-in include:
		HMM-iteration (using HMMER for building an HMM) and guide-tree
		iteration. On top of that HMM input works fine and
		background-frequencies are added to the HHalign process.
		
		Known issues: RNA/DNA alignment is considered buggy. Aligned
		sequences have to be dealigned for HHalign to work properly.
		
		The HMMER version message can be ignored if no HMM-iteration
		was used.