Table 1.

Representative tools for predicting neoantigens that have been published in recent years. The neoantigen type, input data, neoantigen class, HLA typing, immunogenicity score, TAP score and programming language that were used are presented.

Method	Neoantigen Types	Input Data	Neoantigen Class	HLA Typing	Immunogenicity Score	TAP Score	Language	Publish Year
Seq2Neo	SNVs, indels, gene fusions	WES/WGS, RNA-seq	Class I	Yes	Yes	Yes	Python	This study
pVACseq	SNVs, indels, gene fusions	VCF	Class I and II	No	No	No	Python	2019
TSNAD 2	SNVs, indels, gene fusions	WES/WGS, RNA-seq	Class I	Yes	Yes	No	Python	2021
NeoPredPipe	SNVs, indels	VCF, HLA types	Class I and II	No	No	No	Python	2019
Neopepsee	SNVs	VCF, RNA-seq, HLA types	Class I	Yes	Yes	No	Java	2018
nextNEOpi	SNVs, indels, gene fusions	WES/WGS, RNA-seq	Class I and II	Yes	No	No	Nextflow	2021
ProTECT	SNVs	WES/WGS, RNA-seq	Class I and II	Yes	No	No	Python	2020