ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences

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MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics (2019, methodology): “Finally, we used ArwEn version 1.2 (Laslett & Canback, 2007) to detect and annotate tRNA genes.”
tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes (2019, methodology): “5%) classified as possible pseudogenes, or about 2 to 3 false positives per virtual genome, which is consistent with a relatively high false positive rate as previously reported (8).”
MitoFish and MitoAnnotator: A Mitochondrial Genome Database of Fish with an Accurate and Automatic Annotation Pipeline (2013, methodology): “However, in compensation, the heuristics of ARWEN result in a substantial false discovery rate.”
MITOS: improved de novo metazoan mitochondrial genome annotation. (2013, methodology): “Systematic semi-automatic error screening using a list of rules based on tRNAscan-SE (Lowe and Eddy, 1997), ARWEN (Laslett and Canback, 2008), and BLAST (Altschul et al., 1990) searches as well as expert knowledge is used for MitoZoa (Lupi et al., 2010), a recently released new data base.”