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Table 1 Tools and databases used to annotate TEs in the genomes of multicellular eukaryotes published in 2014

From: A call for benchmarking transposable element annotation methods

Genome Homology-based De novo Pipeline  
Repbase RepeatMasker CENSOR RepeatProteinMask RepeatModeler RepeatScout PILER LTR_FINDER LTR_STRUC MITE-Hunter REPET Other Databases Other toolsa Ref.
Phalaenopsis equestris (tropical epiphytic orchid) Plant (monocot)          [81]
Cyprinus carpio (common carp) Animal (bony fish)            TEClass [82]
Esox lucius (northern pike) Animal (bony fish)            Genbank, UniprotKB/SwissProt Custom [83]
Oryza glaberrima (African rice) Plant (monocot)           MSU Repeats, custom (rice-specific) Custom [84]
Callithrix jacchus (common marmoset) Animal (primate)             [85]
Gossypium arboreum (cultivated cotton) Plant (dicot)        [86]
Nicotiana tabacum (common tobacco) Plant (dicot)             TIGR, SGN (Solanaceae-specific)   [87]
Glossina morsitans (tsetse fly) Animal (insect)           Genbank RECON, TARGeT [88]
Oncorhynchus mykiss (rainbow trout) Animal (bony fish)           E-inverted, Manual [89]
Tetrao tetrix (black grouse) Animal (bird)             [90]
Pinus taeda (loblolly pine) Plant (gymnosperm)          PIER 2.0 (conifer-specific) Custom [91]
Spirodela polyrhiza (duckweed) Plant (monocot)             MipsREdat, MIPS PlantsDB Custom [92]
Cynoglossus semilaevis (half-smooth tongue sole) Animal (flatfish)           RepBase (for classification) E-inverted, Custom [93]
Capsicum annuum L. and var. glabriusculum (cult. and wild peppers) Plant (dicot)          MSU repeats   [94]
Capsicum annuum cv. CM334 (hot pepper) Plant (dicot)             [95]
Anopheles sinensis (mosquito) Animal (insect)           Efam (mosquito-specific)   [96]
  1. aNot all tools used in building TE libraries are listed (e.g., UCLUST, MUSCLE)