ParGenes

ParGenes performs massively parallel model selection and maximum-likelihood phylogenetic tree inference across thousands of gene multiple sequence alignments to generate per-gene phylogenies used by coalescent- and reconciliation-based methods.

Key Features:

• Parallel Processing: Executes model-testing and inference on independent MSAs in parallel across supercomputing resources.
• Integrated Model Testing and ML Inference: Integrates model selection with maximum-likelihood (ML) tree inference within a single program invocation.
• Bootstrap and Branch Support Computation: Performs bootstrapping and computes branch support values for inferred gene trees.
• Scalability and Performance: Demonstrated on a 1024-node high-performance computing cluster, inferring over 20,000 gene trees with bootstrap support in approximately 28 hours.
• Per-gene Outputs for Downstream Methods: Produces per-gene phylogenies suitable for input to coalescent- and reconciliation-based species-tree methods.

Scientific Applications:

• Species-tree Reconstruction: Provides per-gene phylogenies required by coalescent- and reconciliation-based approaches for species phylogeny inference.
• Comparative Genomics and Evolutionary Biology: Enables large-scale comparative genomics analyses and inference of evolutionary relationships and gene function across diverse taxa by analyzing thousands of genes simultaneously.

Methodology:

Performs model-testing and maximum-likelihood inference on independent MSAs in a parallelized manner, including bootstrapping and computation of branch support values.