Seq2Logo-2.0: Release notes:                                       22 March 2014
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* Seq2Logo has been completely rewritten to make it easier maintainable and
  allow more flexibility.
  
* Most of the script now uses a faster algorithm which should be noticeable
  for those creating long motifs.
  
* Enabled the use of PSSM inputs with 2-50 columns, compared to the limit of
  2-20 amino acids previously. This was done to allow the use of a column for
  showing gaps in the PSSM motif primarily.
  
* Fixed a limitation of PSSM inputs where a PSSM with no position number and
  where the weights were presented as integers resulted in the first column to
  be interpreted as the position number. Now Seq2Logo relies on the header
  line containing the characters to determine if the first position is a
  position number or a weight.
  
* Reduced alphabet limitations. It is now possible to use more symbols and not
  only the amino acids symbols. Note: Remember to upload a new backgound
  frequency table, and also a new substitution matrix if you use pseudo
  counts.
  
* PSSM inputs can now use all ASCII symbols available.
  
* Fixed poscript scaling and repositioning for all symbols. Now all symbols
  should fit their appointed bounding boxes.
  
* Fixed a Postscript zero division problem occuring when there were no
  positive values in the PSSM.
  
* Fixed a Postscript zero division problem caused by small height values.
  
* Integration of DNA sequence input interpretation and calculations. It is now
  possible to upload DNA sequence alignments and get a sequence motif using
  Seq2Logo. Note: Seq2Logo does neither have any default transition table or
  reference distributions for nucleotides, so the user should either provide
  these themselves or set beta to 0 and chose the Shannon logo.
  
* A more flexible and intuitive color tool has been added, giving the user
  more power over the visual setup of the motif.
  
* Thorough documentation has been added to the source code, the commandline
  interface has been updated, and these realease notes are now available from
  the web.
  
* The Hobohm 1 algorithm has been upgraded to sort the alignment sequences so
  the sequences with most data (eg. least amount of gaps) are first, and
  those with many gaps are added in the end. This fixes an issue where a
  sequence with many gaps attracted to many sequences to its cluster, and
  where these sequences in the final cluster could be quite dissimilar.
  
* The Blosum matrix and background frequency file upload can now also be
  copy/pasted just like the file upload, by clicking the blue 'switch' link.
  
* An option for adding the consensus sequence to the x-axis position numbers
  is now available in the advanced menu.
  
* The settings menu on the output page has had a small change. It is now
  possible to download the used BLOSUM substitution matrix and the background
  frequencies.
  
* The use of a position specific reference distribution (background
  frequencies) is now possible. The reference distribution format has been
  adjusted so it works with the same setup as PSSM input files.
  Note: To specify a global distribution for all positions, just upload a file
  containing only one distribution line (i.e. first position).
  Additionally, any missing positions or positions containing a 0 or a
  negative value, will be overridden to use a flat/uniform distribution. A user
  warning is recorded and can be found in the warning section of the output
  page if this is true.
  
* It is now possible to pipe the input to Seq2Logo instead of using the -f
  argument. See the readme for an example hereof.