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v4.3 released July, 2021
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 - Use -k flag or AltEst.Reference to load a reference annotation and predict the splicing variants. 
 - Improve performance to perform the variant prediction.
 - In the AltEst plugin, add the parameter 'AltEst.IncompatibilityExonBorderMatchThreshold'. EuGene will perform a 
   variant search only for the AltEst where one of the exons shows at one of its borders a difference of at least 
   x nucleotides with a reference gene.
 - If AltEst is activated, create two files: one for the initial prediction (.gff3) and one also including the variants
   (.variants.gff3)
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v4.2b released Sep. 2020
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In the Est plugin change the way the transcript strand is chosen. Previously ejected transcripts are now kept.

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v4.2a released Dec. 2016
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- new plugin 'SignalWAM' to predict spliced|start signals with weight-array matrix
- In the Est plugin, change the sorting function: for the same number of gaps, select first the smallest covered region.

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v4.1c released Sept. 2014
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Improve GFF3 output format: remove ending tab.
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v4.1c released Janv. 2014
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non canonical splice sites allowed
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v4.0a released Juil. 2011
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* EuGene is able to annotate prokarotic sequence. It can predict overlapping protein genes (on the same strand or not), unstranslated transcribed internal regions and operon structure.
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v3.6 released Fevr. 2010
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EuGene can now predict non protein coding RNA.

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v3.3 released 2 Sept. 2005
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* Output.cc Output.h disapear. Now eugene textual outputs are printed by Prediction class.

* Multiple textual output are possible by using -pa|d|g|h|l|s|o (example:-phg for a gff and html output)
  Each -p create a file composed by the name of the input fasta file + an extension .gff or .html ...

* For each prediction a *.misc_info file is created. This file contains some informations of the prediction and the postprocess (-E -B)

* The -g argument to activate the graphical output not take argument now.

* New parameter in the eugene.par to print intron in the textual output : Output.intron
	

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v3.2 released 1 Apr. 2005 
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* change the use of the software:
	EUGENEDIR: environment variable updating with the eugene root repertory
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        (default value /usr/local/share/eugene). This repertory contains repertories:
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	     - cfg (with eugene.par the default parameter file)
	     - models (provided models)
	     - doc (documentation)
	     - plugins 
	     - web (to vizualize eugene HTML outputs)

* Allow MAC compilation

* no more need to call the CREATE_LINKS procedure.

* Tests as compilation are called in the root directory.

* HTML outputs reference local web directory and no more WEB in the current directory.

* Optimized parameter file is written in the current directory instead of the directory of the parameter file used.

* New parameter Output.webdir indicating where to find files necessary to vizualize HTML outputs ('LOCAL' value to use the local web directory or a URL)
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* debug related to gene number (due to UTR intron)

* debug related of stop just before a splice site

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v3.1 released 3 Feb. 2005 
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* new plugin PepSignal
* new procedures:
    - Procedures/Get/egn_compseq.pl (counts composition of dimer/trimer/etc words)
    - Procedures/Get/getRepeat4eugene.pl (build .ig files)
* new parameters defined:
   - EuGene.sloppy: if 1 then some sensors files can be missing
   - EuGene.SplicedStopPen: penalty for predicting genes containing in-frame spliced STOPs
   - Output.MinCDSLen: specify the minimum length of CDS in nucleotid
   - Est.MinDangling: minimum length of the first and last match region in a genomic spliced alignment
   - EstMaxIntron: maximum length for the first and last gap (intron) in a spliced alignment
   - SMachine.isScaled: indicates if prediction is scaled after fitsigmoid in SpliceMachine
   - Tester.SPSN.Eval: defines the type of the considering signal
* use of 1 and 0 instead of TRUE and FALSE in the parameters file (old values are still accepted)
* new argument -A <parameter file name>
* no more librairies are provided (they have to be on the system)
* debug and improvement of the Est sensor (takes into account UTR introns), 
  the Repeat sensor (exit if the .ig files contain overlapped or non sorted repeats)
* modification of the compilation arguments
* little modification of the HTML output
* update in documentation
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v3.0 released 21 Oct. 2004 
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