ExaML

ExaML infers phylogenies from large-scale whole-transcriptome and whole-genome alignments using high-performance computing for phylogenomic analyses.

Key Features:

• Substitution models and data types: ExaML version 3 supports a broader range of substitution models and data types for more flexible phylogenetic analyses.
• Load balancing algorithm: Integrates a novel load balancing algorithm to optimize computational efficiency across multiple processors.
• Parallel I/O optimization: Implements parallel input/output optimizations to accelerate data read/write operations in multi-processor environments.
• Intel MIC-based hardware support: Provides a production-level implementation for Intel Many Integrated Core (MIC) architectures to exploit their parallelism.
• Scalability on supercomputers: Leverages supercomputing resources to handle the large datasets typical of phylogenomic studies.
• Next-generation sequencing compatibility: Applicable to alignments derived from next-generation sequencing technologies.

Scientific Applications:

• Whole-transcriptome phylogenetics: Inferring evolutionary relationships from whole-transcriptome alignments.
• Whole-genome phylogenetics: Inferring evolutionary relationships from whole-genome alignments.
• Phylogenomics of NGS datasets: Conducting phylogenomic analyses on large datasets generated by next-generation sequencing technologies.
• High-performance phylogenetic inference: Scaling phylogenetic computations on supercomputers and Intel MIC platforms.

Methodology:

Infers phylogenies from whole-transcriptome and whole-genome alignments, supports multiple substitution models and data types, and employs a load balancing algorithm, parallel I/O optimizations, and a production-level Intel MIC implementation to scale on supercomputers.