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Table 3 Comparison of 8 sequence simulation methods

From: SimSpliceEvol: alternative splicing-aware simulation of biological sequence evolution

 ROSEDawgSIMPROTEvolveAGene3iSGv2.0INDELiblePhyloSimSimSpliceEvol
Data simulated
 Exon-intron structure    XXXX
 Splice sites      XX
 Alternative transcripts       X
 Coding sequence   XXXXX
 Non-coding sequenceXX XXXXX
 Protein sequenceX XXaXXXXa
 Sequence alignmentXXXXXXXX
 Splicing ortholog groups       X
Evolution simulated
 Exon-intron structure       X
 Splice sites      X 
 Alternative transcripts       X
 Coding sequence   XXXXX
 Non-coding sequenceXX XXXXX
 Protein sequenceX X XXX 
 Heterogeneous evolution (partition) XX XXXXb
 lineage-specific motif conservation    X   
 Length-specific motif conservationX   X   
 Site-specific motif conservation    XXX 
Indel treatment
 ContinuousXXXX   X
 Dynamic length adjustment X  XXXX
 Event tracking    XXXX
 Probability of ins and del independentXX XXXXX
 Empirical length distribution XXXXXXX
  1. a The methods can generate amino acid sequences, but the simulation is done only at the nucleotide level. b The method defines partitions that evolve under two distinct models for exon and intron, but within an exon or an intron segment, the evolution is homogeneous. Features that are specific to SimSpliceEvol are indicated in bold characters