Tools	Whether to add and reasons	Latest version	Methods	Category	Installation	Language	Reference	Year of reference	Source
Ribotricer	YES.	1.3.1	Normalized projected vector	Frame pattern consistency	Conda	Python3	[1]	2019	https://github.com/smithlabcode/ribotricer
RiboCode	YES.	1.2.11	Wilcox single rank test	Frame preference	Conda	Python2	[2]	2018	https://github.com/xryanglab/RiboCode
RiboTaper	YES.	1.3.1a	Fourier transform via multitaper method	Frame preference and 3-nt periodicity frequency	Conda	Shell and R	[3]	2016
ORFscore	YES.	NA	Chi-square test	Frame preference	Contained in RIboTaper	NA	[4]	2014
RP-BP	YES.	2.0.0	Two-component mixture model	Frame pattern consistency	Git-Hub	Python3	[5]	2017
ORF-RATER	YES.	Version in Git-Hub	Non-negative least squares regression and a random forest classifier	Aggregated coverage features of ORF	Git-Hub	Python2	[6]	2015	https://github.com/alexfields/ORF-RATER
RibORF	YES.	1.0	Percentage maximum entropy	Frame preference and uniform coverage	Git-Hub	Perl	[7]	2015
RiboWave	YES.	1.0	Wavelet transform	Frame preference and 3-nt periodicity frequency	Git-Hub	Shell and R	[8]	2018	https://github.com/lulab/Ribowave
Ribo-TISH	YES.	0.2.4	One-tailed Wilcoxon rank-sum test	Frame preference	Git-Hub/Pip	Python2/3	[9]	2017	https://github.com/zhpn1024/ribotish
plastid	YES. QC	0.48	calculate the profile of the RPF 5′ end distribution	Custom selection	Pip	Python2	[10]	2016	https://pypi.org/project/plastid/
Ribo-seQC	YES. QC	0.99.0	Frame preference or progressively add more accurate in-frame signals	Frame preference	Git-Hub	R	[11]	bioRxiv	https://github.com/lcalviell/Ribo-seQC
riboWaltz	YES. QC	1.1.0	calculate the profile of the RPF 5′ end distribution	Frame preference or custom selection	Git-Hub	R	[12]	2018	https://github.com/LabTranslationalArchitectomics/riboWaltz
Shoelaces	YES. QC				Pip				https://bitbucket.org/valenlab/shoelaces/src/master/
RiboProfiling	YES. QC				Bioconduct	R		2016	https://www.bioconductor.org/packages/release/bioc/html/RiboProfiling.html
RUST	No. QC (only one offset)				Supplementary file	python		2016	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5059445/
RiboViz	No. QC (only hisat2)				Git-Hub	R		2017	https://github.com/riboviz/riboviz/blob/master/docs/user/prep-riboviz-operation.md
riboSeqR	No. QC (no offset)				Bioconductor	R		2015	http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html
systemPipeR	No. QC (only end to end)				Bioconductor	R		2016	http://bioconductor.org/packages/devel/bioc/html/systemPipeR.html
RiboHMM	YES.	Version in Git-Hub	Hidden Markov model (HMM)	Aggregated coverage features of ORF	Git-Hub	Python2	[13]	2016
DeepRibo	YES.	Version in Git-Hub	convolutional neural networks and recurrent neural networks	Frame preference and features of specific sequence	Git-Hub	Python3	[14]	2019
SaTAnn	YES.	0.99.0	P-site interpretability and multitaper method	Transcript filter and the same as RiboTaper	R	R	[15]	bioRxiv	https://github.com/lcalviell/SaTAnn
AltORFev	YES.	Version in the source	Linear scanning mechanism and its modifications (leaky scanning, reinitiation)	Nucleotide context of the start codons.	Web/BioJava	Web/ Java1.8	[16]	2016	http://www.bionet.nsc.ru/AUGWeb/
PRICE (GEDI)	YES.	1.0.3b	Hypothesis tests based on the generalized binomial distribution	Frame preference	Git-hub	Java1.8	[17]	2018	https://github.com/erhard-lab/gedi/wiki/Price
SPECtre	YES.	Version in Git-hub	Spectral coherence	3-nt periodicity frequency	Git-hub	Python3	[18]	2016	https://github.com/mills-lab/spectre
FLOSS	NO.	NA	Footprint size distributions among different subunit	Distribution of footprint length	Contained in SPECtre	NA	[19]	2014	Contained in SPECtre
PTS and CSCPD	NO. Just a implement which find frame shifting or dual coding regions.	Version in the source	Calculating in-frame P-site proportion in sliding windows	Frame preference	In supplemental files of the article	R scrpit	[20]	2012	https://genome.cshlp.org/content/22/11/2219/suppl/DC1
TE	NO.	NA	The ratio of RPF and each ORF with mRNA-seq	Translational efficiency	NA	NA	[21]	2009	NA
ORF coding score	NO.	NA	Mean of normalized translational efficiency of hexamers between ORF and intron region	Translational efficiency	NA	NA	[22]	2014	NA
RRS	NO. Just a metric inferring translation via the relationship between ORF and UTR sequence in downstream.	Version in the source	The ratio of each ORF coverage with coverage after stop codon of this ORF corrected by mRNA-seq	Coverage after stop codon	Web	Java	[23]	2013	http://guttmanlab.caltech.edu/software/RRS.jar
uORF-Tools	NO. Just pipeline using Ribo-TISH.	5.4.5	Ribo-TISH method	The same as Ribo-TISH	Git-hub	Snakemake	[24]	2019	https://github.com/Biochemistry1-FFM/uORF-Tools
TOC	NO. No available source.	NA	A random forest classifier with four metrics.	Translational efficiency, coverage ratio, ORF length ratio	NA	NA	[25]	2013	NA