Table 1.

Overview of identified ORF detection tools. Most tools make no statement about the taxonomic domain they were developed for. Some, however, utilize eukaryotic data as proof-of-principle (indicated by ). The first eight tools were benchmarked in this manuscript.

Name	Input data	Method	Availability	Taxonomy
DeepRibo [41]	Ribo-seq	Deep Learning	github	Prokaryotes
REPARATION_blast [42]	Ribo-seq	Random Forest	bioconda, github	Prokaryotes
SPECtre [37]	Ribo-seq	Spectral Coherence	github	Eukaryotes
Ribo-TISH [36]	Ribo-seq	Negative Binominal Test	bioconda, github	Eukaryotes
IRSOM [21]	RNA-seq	Self-Organizing Map	gitlab, webservice	Eu-, Prokaryotes
smORFer [44]	Ribo-seq	Fourier transform	github	Eu-, Prokaryotes
PRICE [38]	Ribo-seq	EM-algorithm and statistical testing	github	Eukaryotes
ribotricer [39]	Ribo-seq	3D to 2D projection for periodicity	bioconda, github	Eukaryotes
RiboTaper [47]	Ribo-/RNA-seq	Multitaper Spectral Analysis	bioconda, galaxy	Eukaryotes
RiboHMM [48]	Ribo-/RNA-seq	Hidden Markov Models	github	Eukaryotes
ORFrater [49]	Ribo-seq	Linear Regression	github	Eukaryotes
RibORF [50]	Ribo-seq	Logistic Regression	github	Eukaryotes
Rp-Bp [51]	Ribo-seq	Markov Chain–Monte Carlo	github	Eukaryotes