SimSpliceEvol

SimSpliceEvol simulates the evolution of coding sequences and exon-intron structures with explicit modeling of alternative splicing to generate spliced transcript variants along an input gene tree for benchmarking splice-aware analyses.

Key Features:

• Alternative Splicing Simulation: Simulates alternative splicing events that produce multiple transcript variants from eukaryotic coding genes.
• Exon-Intron Structure Evolution: Models changes in exon-intron structures over evolutionary time.
• Traditional Sequence Evolution: Simulates traditional sequence evolution events such as mutations.
• Gene Tree-Based Simulation: Operates along the branches of an input gene tree to simulate evolutionary events across lineages.
• Spliced Sequence Analysis Data Generation: Generates datasets for testing spliced alignment of cDNA and genomic sequences, multiple cDNA alignments, identification of orthologous exons, inference of splicing orthology, and transcript phylogeny inference.
• Implementation: Implemented in Python.

Scientific Applications:

• Benchmarking aligners: Benchmarking splice-aware alignment of cDNA to genomic sequences and multiple cDNA alignment methods.
• Orthology inference testing: Assessing methods for identification of orthologous exons and inference of splicing orthology.
• Transcript phylogeny evaluation: Evaluating methods for inferring transcript phylogenies.
• Simulated data provision: Producing realistic simulated datasets for testing computational tools that analyze spliced RNA sequences.

Methodology:

Simulates traditional sequence evolution events (e.g., mutations), alternative splicing events, and exon-intron structure changes along branches of an input gene tree.