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%           BRAKER2                                                                               %
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%           Authors: Lars Gabriel, Katharina J. Hoff, Tomas Bruna, Simone Lange,                  %
%                    Alexandre Lomsadze, Mark Borodovsky, Mario Stanke                            %
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%           Contact: [email protected]                                             %
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%           Date: November 7th 2022                                                               %
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  1.  INTRODUCTION
  2.  INSTALLATION & FURTHER INFORMATION

              1. INTRODUCTION
              ---------------
The rapidly growing number of sequenced genomes requires fully automated methods for accurate gene
structure annotation. With this goal in mind, we have developed BRAKER1 [Hoff et al., 2015], a 
combination of GeneMark-ET [Lomsadze et al., 2014] and AUGUSTUS [Stanke et al., 2008, Stanke et al., 
2006], that uses genomic and RNA-Seq data to automatically generate full gene structure annotations 
in novel genomes.
However, the quality of RNA-Seq data that is available for annotating a novel genome is variable, and
in some cases, RNA-Seq data is not available, at all. BRAKER2 is an extension of BRAKER1 which 
allows for fully automated training of the gene prediction tools GeneMark-EX [Lomsadze et al., 2005,
Ter-Hovhannisyan et al., 2008, Lomsadze et al., 2014] and AUGUSTUS from RNA-Seq and/or protein 
homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology 
information into the prediction.
In contrast to other available methods that rely on protein homology information, BRAKER2 reaches
high gene prediction accuracy even in the absence of the annotation of very closely related species 
and in the absence of RNA-Seq data.
BRAKER3 can combine RNA-Seq and protein homology information.


              2. INSTALLATION & FURTHER INFORMATION
              ---------------

Installation instructions and further information on running BRAKER, bug reporting, citing BRAKER
are provided in ../README.md.