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The GALBA pipeline. Miniprot performs rapid spliced alignment of proteins against the genome. Subsequently, miniprothint (2) scores and classifies these alignments. Training genes for AUGUSTUS are generated from the best high quality miniprot alignment per locus (1). After training, AUGUSTUS predicts genes using the alignment evidence generated by miniprothint. AUGUSTUS parameters are refined by one iteration of training (3). The numbering of steps in the figure caption corresponds to the order in which steps were introduced into GALBA during development, see Additional file 1 : Results section S4.1

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