List of changes from version 2.5 to 2.5.5 (until March 2nd, 2011)
     - added a tutorial
     - bugfixes, in particular one that caused a crash on Mac OS
     - new species verticillium, honeybee, butterfly
     - option --noprediction=1 to score input gene structures
     - adjust autoAug.pl to new PASA version
List of changes from version 2.4 to 2.5 (until Nov 13th, 2010)
     - first release of protein profile extension (PPX)
     - scripts added for PPX:
       msa2prfl.pl: converts MSAs in FASTA/CLUSTAL format to protein profiles to use with AUGUSTUS
       block2prfl.pl: converts BLOCKS database flat file to protein profile
       del_from_prfl.pl: manually delete blocks from profile
     - executables added for PPX: 
       prepareAlign: eliminates gap-rich sequences from FASTA MSA
       fastBlockSearch: performs a preliminary profile search to determine regions for gene prediction
     - PPX-specific new parameters are:
       /ProteinModel/allow_truncated: allows profile hits in right-truncated genes
       /ProteinModel/block[part]_threshold_{sens,spec}: set model specificity/sensitivity
       /ProteinModel/weight: set weighting of protein model vs. ab-initio model
     - PPX is introduced and can be used with parameter --proteinprofile
     - new species pneumocystis (fungus), user contributed by Marco Pagni
List of changes from version 2.3.1 to 2.4 (until July 27, 2010)
     - improved human parameter set: roughly 13 percent points better on CDS exon level
     - improved fly paramter set
     - added new species 'lamprey', contributed by Falk Hildebrand and Shigehiro Kuraku
     - added new species Leishmania tarentolae, Trichinella spiralis
     - added maize5 parameter set, better than 'maize' and with UTR model
     - the GC content parameter class is now chosen locally, instead of using a constant
       GC constant for each sequence or sequence chunk, performance improvement in human
     - bugfix in aln2wig that caused a segmentation fault
     - bugfix in etraining when using alternative translation tables
     - introduce local splice site malus, that is effective when neighboring region has exonic evidence
     - bugfix in etraining that concerns the weighting of training examples
       the fix increases e.g. in C.elegans accuracy by 1.5 percent points on the exon level
       and 4.2 percent points on the gene level
     - added new script gtf2gff to convert gtf output (e.g. from Augustus) to gff3
       or to switch between the two UTR representations (explicit UTR vs exon)
     - added script intron2exex.pl for iterative RNA-Seq alignments
     - option --pairbed to filterPSL.pl for creating genicpart hints from read pairing information
     - allow to tie intergenic content model to intron content model with tieIgenicIntron in training
     - bugfix: intron/igenic content model was partially trained from UTR regions
     - fixed a bug that occurred when a sequence contained nothing but N's
     - fixed bug in intronmodel training that occurs when UTRs are turned on
     - fixed pasa to polyA hints bugs in autoAug.pl
List of changes from version 2.2 to version 2.3 (until November 1st, 2009):
     - added capability and documentation for incorporating RNA-Seq
     - added aln2wig program which summarizes psl and shrimp format to wig
     - speed up script makeUtrTrainingSet.pl
     - hints can now have a mult=n feature in the last column to specify multiplicity=copy number
     - added local malus for punishing unevenly supported exon candidates
     - gff2gbSmallDNA.pl now allows for gff3 input
     - getAnnoFasta.pl now also prints coding sequence and mRNA derived from genome sequence
     - script polyA2hints.pl for hints from polyA position file
     - updated blat2hints: for intron hints from RNA-Seq and for transcript termini
     - parameter /IntronModel/dss_consensus_gc_prob now allows gc-ag introns also in absense of hints
     - autoAug pipeline now includes polyA hints from PASA
     - parameter allow_hinted_splicesites allows other non-standard splice sites, such as ac-at
     - bugfixes (in particular in response to MAC users compilation problems)

List of changes from version 2.1 to version 2.2 (until June 26th, 2009):
     - release of the autoAug*.pl scripts for automatic training and prediction for new genomes
     - new genemodel 'intronless' for prokaryotes and eukaryotes withouth introns

List of changes from version 2.0.3 to version 2.1 (until March 11th, 2009):
     - updated species: Chlamydomonas reinhardtii
     - new species: Acyrthosiphon pisum (pea aphid)
     - packaged more scripts that are useful for training 
     - new hint type genicpart = nonirpart
     - introduce fuzzyness in dss and ass hints
     - reduced memory usage
     - allow other poly(A) signal consensus than aataaa
     - fixed some format violations when outputting gff3
     - allow general alternative codon to amino acid translation tables (parameter translation_table)

List of changes from version 2.0.2 to version 2.0.3 (until March 13th, 2008):
     - new species: Chlamydomonas reinhardtii (green algae)
     - new species: Nasonia vitripennis (wasp)
     - new species: Solanum lycopersicum (tomato) 
     - new species: Amphimedon queenslandica (sponge)
     - in fasta headers (">") the name is considered only to go up to the first white space

List of changes from version 2.0.1 to version 2.0.2 (until May 30th, 2007):

     - a gene can now be truncated in the middle of an exon or an intron.
       This is helpful when many genes are only partially sequenced, e.g. when searching genes/exons
       in the raw DNA reads.
     - Augustus retrained for Arabidopsis thaliana, Galdieria sulphuraria and Caenorhabditis elegans.
     - fixed bug that no spliced 5'UTR was predicted on the reverse strand except at sequence boundaries
     - optimize_augustus.pl now also allows to automatically optimize the transition matrix
     - fixed bug. before some hints were ignored when the contig was shorter than 2000bp
     - option --uniqueGeneId=true adds the sequence name to the gene name
 
List of changes from version 2.0 to version 2.0.1 (until January 30th, 2007):
     - genemodel=complete works now with UTR
     - added several scripts for generating hints (from blat, retrogenes, transmap, exoniphy) and
     for creating cluster jobs
     - fixed bug with intronpart hints upvaluing a few non-intron bases in UTR
     - can now combine --genemodel=complete with UTR predictions
     - fixed crash that occurred when a genbank file had annotation with negative coordinates.
     - fixed problem with toxoplasma UTR transition matrix (added the 4 extra UTR intron states)
     - fixed problem with galdieria UTR model (TTSMOTIF was missing)

List of changes from version 1.8.2 to version 2.0 (until January 8th, 2007):

     - predict 5'UTR and 3'UTR including introns (available for human, galdieria, toxoplasma,
     caenorhabditis)
     - evidence-based alternative transcripts
     - new types of hints: tss, tts, CDS, CDSpart, UTR, UTRpart, irpart, nonexonpart
     - hints can be summarized to groups
     - hints can have a priority
     - long input sequence is split taking hints into account
     - 32 new fungi species
     - output in gff3 format possible
     - speed improvement by 12% (comparison operator)
     - a subwindow for predictions can be specified
     - subdirectory structure of config directory
     - new species: toxoplasma gondii

List of changes from version 1.8 to version 1.8.2 (until March 10th, 2006):

     - new species: Zea mays (maize)
     - Species parameters contributed by Jason Stajich: Caenorhabditis
       elegans, Saccharomyces cerevisiae, Ustilago maydis, Phanerochaete
       chrysosporium, Neurospora crassa, Histoplasma capsulatum, Fusarium
       graminearium, Cryptococcus neoformans, Aspergillus nidulans

List of changes from version 1.7 to version 1.8 (until January 18th, 2006):

     - new species: Schistosoma mansoni, Tetrahymena thermophila, Galdieria sulphuraria
     - enabled non-standard set of stop codons (in Tetrahymena thermophila TAG and TAA are coding)
     - frequencies of the 3 stop codons configurable
     - option: AUGUSTUS_CONFIG_PATH can be set on the command line
     - some filtering of the Viterbi prediction with respect to posterior probabilities 

List of changes from version 1.6 to version 1.7 (until October 5th, 2005):

     - automatized training for new species
     - alternative transcripts
     - posterior probability of exons, introns, transcripts and genes is reported
     - fixed bug that predicted splice sites just outside the sequence boundaries
     - added the option of outputing the predicted coding sequence

List of changes from version 1.5 to version 1.6 (until August 3rd, 2005):

     - The source code is now freely available (Artistic Licence).
     - New species: Tribolium castaneum, Aedes aegypti, Coprinus cinereus
     - Bugfix: Wrong interpretation of reading frame for reverse strand exon hints.
     - Training of hints possible with nested genes.
     - Renaming StateType 'single' to 'singleG' to avoid compilation conflicts on some machines
     - Bugfix: Exon hints and exonpart hints including the stop codon were missed for reverse terminal or reverse single exons.
     - Changed output format to gtf. Includes a (redundant) transcript_id now.
     - Check consistency of hints with the sequence and output warnings for inconsistencies.
     - Bugfix: Rare bug in aSSProb that caused Viterbi to get stuck.
     - Bugfix: Check sequence bounds, when probing for a splice site. Bug had caused a segmentation fault.

List of changes from version 1.4 to version 1.5 (until 12/04):

     - New species: Brugia malayi.
     - Training can now take sequences with multiple genes on both strands.
     - The use of hints has been documented.

List of changes from version 1.3 to version 1.4 (after 06/04):

     - New species: Arabidopsis Thaliana.
     - More standard, user friendly program call. No need to specify a configuration file anymore.
     - Fixed bug for the emission probabilities of exonpart pitchfork hints in exons which are supported
       by exonpart hints. Now AUGUSTUS has an incentive to predict an exon which is as small as possible even
       when an exonpart hint supports it.
     - Fixed rare bug with exon state at end of DNA.
     - Optimized meta parameters for human.

List of changes from version 1.2 to version 1.3:

     - avoid predicting exons with in-frame stop codons at the splice sites
     - accuracy of extrinsic information can now be checked on multi-gene sequences

List of changes from version 1.0 to version 1.2:

     - Added reference information to the text output.
     - Bugfix: The last line of an input file which contains no newline at the end was
       read twice.
