GenNon-h

GenNon-h generates multiple DNA sequence alignments by simulating sequence evolution on phylogenetic trees using discrete-time probability substitution matrices to model nonhomogeneous and nonstationary processes.

Key Features:

• Discrete-Time Markov Processes: Simulates sequence evolution under discrete-time Markov models rather than continuous-time frameworks.
• Probability Substitution Matrices: Generates MSAs directly from probability substitution matrices that specify nucleotide substitution probabilities.
• Nonhomogeneous Data Generation: Supports assignment of distinct substitution rates or matrices across different lineages of a phylogenetic tree.
• Phylogenetic Tree Input: Accepts trees in Newick format with branch lengths given as the expected number of substitutions per site.
• Nonstationary Data Simulation: Produces data with nonstationary nucleotide composition across the tree.

Scientific Applications:

• Hypothesis Testing: Generates datasets to test hypotheses that require nonhomogeneous or nonstationary evolutionary models.
• Algorithm Robustness Evaluation: Creates challenging simulated data for assessing the performance of phylogenetic reconstruction algorithms.
• Exploration of Evolutionary Models: Enables investigation of how different discrete-time substitution assumptions affect sequence evolution predictions.

Methodology:

Simulates MSAs directly from probability substitution matrices under discrete-time Markov processes using input models and phylogenetic trees (Newick with branch lengths as expected substitutions per site) to produce DNA alignments of specified length and to handle nonhomogeneous and nonstationary substitution processes.