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Improvement in the intron annotation step with the possibility of finding introns in ribosomal RNA genes.
Mitochondrial contig are now sorted by hit score (with mtDNA_contig_1 having a better score than mtDNA_contig_2 ...). Associated new option: --max-hit. This option allows to specify how many contig at most MitoFinder will annotate.
New option --rename-contig (to rename or not the contig(s) matching the reference).
New option --adjust-direction(to adjust the direction of the contig(s) matching the reference, if necessary).
New option --citation(to know how to cite MitoFinder).