Table 1.

Technical comparison among existing orthologues mapping methods.

Method	Sequence alignment	Epigenomic features	Sequence grammar features	Scalability	Running time	Generalizability
AdaLiftOver	Yes	Multiple	Yes	Yes	∼20 min	Yes
bnMapper (Denas et al. 2015)	Yes	No	No	Yes	∼10 min	Yes
EpiAlignment (Lu et al. 2019)	Yes	One	No	No	∼3 h	No
UCSC liftOver (Hinrichs et al. 2006)	Yes	No	No	Yes	∼10 s	Yes

Sequence alignment: the dependence on the UCSC sequence alignment framework. Running time: the average running time for ∼20 000 TF ChIP-seq peaks. Generalizability: whether or not the method supports any genomes with chain files.