MySSP

MySSP simulates DNA sequence evolution along phylogenetic trees, modeling insertions and deletions (indels), non-stationary evolutionary patterns, and producing ancestral sequences for evolutionary analysis.

Key Features:

• Inclusion of Indels: Incorporates insertions and deletions into sequence simulations to represent structural changes in DNA over time.
• Non-Stationary Patterns: Allows modeling of non-stationary evolutionary patterns with rates and patterns that can vary across branches or periods of a phylogenetic tree.
• Output of Ancestral Sequences: Generates reconstructed ancestral sequences from simulated data for downstream evolutionary inference.

Scientific Applications:

• Phylogenetic Analysis: Provides simulated sequence data for development and testing of phylogenetic models and tree-inference methods.
• Evolutionary Studies: Enables exploration of complex evolutionary processes such as indel dynamics, adaptive changes, and lineage-specific rate shifts.
• Ancestral Sequence Reconstruction: Supplies ancestral sequences to support studies of functional evolution of genes and proteins.

Methodology:

MySSP uses a simulation framework that integrates evolutionary processes across phylogenetic trees and accommodates models including indels and variable (non-stationary) evolutionary rates, producing simulated sequences and ancestral reconstructions.