indel-Seq-Gen

indel-Seq-Gen simulates evolution of DNA and protein sequences to model insertions and deletions, motif conservation, subsequence-length constraints, and lineage-specific divergence for studies of divergent DNA and protein superfamilies.

Key Features:

• Lineage-specific evolutionary models: Implements lineage-specific substitution and evolutionary models to simulate divergence across different phylogenetic branches.
• Motif conservation with PROSITE-like regular expressions: Enforces motif conservation using PROSITE-like regular expressions to preserve functional sequence patterns.
• Indel tracking and discrete stepping procedure: Tracks insertions and deletions and uses a discrete stepping procedure to correct bias in indel modeling.
• Subsequence-length constraints: Applies constraints on subsequence lengths to mimic length-specific evolutionary pressures.
• Coding and noncoding DNA simulation: Supports simulation of both coding and noncoding DNA evolution.

Scientific Applications:

• Hypothesis validation: Validates biological hypotheses that require complex sequence simulations beyond homogeneous models.
• Modeling heterogeneous evolutionary processes: Models local similarities, motif conservation, and heterogeneous evolutionary dynamics within sequences.
• Phylogenetic and protein superfamily divergence studies: Simulates lineage-specific evolution for analyses of phylogenetic relationships and protein superfamily divergence.
• Benchmarking simulation methods: Enables comparison of simulated sequences against alternative models, exemplified by simulations of calycin-superfamily sequences.

Methodology:

Formalizes sequence representation, implements lineage-specific evolutionary models, enforces subsequence-length constraints, applies PROSITE-like regular expressions for motif conservation, and uses a discrete stepping procedure to model and correct biases in indel events.