Table 3 Comparison of 8 sequence simulation methods

Data simulated

 Exon-intron structure

X

X

X

X

 Splice sites

X

X

 Alternative transcripts

X

 Coding sequence

X

X

X

X

X

 Non-coding sequence

X

X

X

X

X

X

X

 Protein sequence

X

X

X^a

X

X

X

X^a

 Sequence alignment

X

X

X

X

X

X

X

X

 Splicing ortholog groups

X

Evolution simulated

 Exon-intron structure

X

 Splice sites

X

 Alternative transcripts

X

 Coding sequence

X

X

X

X

X

 Non-coding sequence

X

X

X

X

X

X

X

 Protein sequence

X

X

X

X

X

 Heterogeneous evolution (partition)

X

X

X

X

X

X^b

 lineage-specific motif conservation

X

 Length-specific motif conservation

X

X

 Site-specific motif conservation

X

X

X

Indel treatment

 Continuous

X

X

X

X

X

 Dynamic length adjustment

X

X

X

X

X

 Event tracking

X

X

X

X

 Probability of ins and del independent

X

X

X

X

X

X

X

 Empirical length distribution

X

X

X

X

X

X

X