GeLL

GeLL provides a Java library for defining substitution models and computing phylogenetic likelihoods to support model development, parameter optimization, ancestral state reconstruction, and sequence simulation.

Key Features:

• Model Flexibility: Support for defining a wide range of substitution models, including mixture models and non-reversible models, via text-based model specifications.
• Discrete Data Specification: Ability to specify novel forms of discrete data for tailored phylogenetic analyses.
• Likelihood Calculations: Classes dedicated to computing likelihoods for phylogenetic inference under user-defined models.
• Parameter and Branch-Length Optimization: Tools for optimizing model parameters and branch lengths to fit sequence data.
• Ancestral State Reconstruction: Functionality for reconstructing ancestral states across phylogenies.
• Sequence Simulation: Capabilities to simulate synthetic sequence datasets under specified models.
• Java Implementation: Implemented in Java, providing programmatic classes and data structures for model and likelihood operations.

Scientific Applications:

• Substitution Model Development: Development and implementation of novel substitution models for molecular-evolution studies.
• Molecular Evolution Inference: Estimation of evolutionary relationships and investigation of mechanisms driving sequence change using likelihood-based approaches.
• Ancestral Reconstruction Studies: Inference of genetic states of common ancestors within phylogenies.
• Method Validation and Simulation: Generation of simulated sequence datasets to test hypotheses and validate analytical methods.

Methodology:

Implemented in Java with text-based model and discrete-data specification; includes classes for likelihood calculation, parameter and branch-length optimization, ancestral state reconstruction, and sequence simulation.