AI Article Synopsis
- Phylogenetic analysis is becoming crucial in medical and biological research, fueled by the rapid growth of datasets from next-generation sequencing.
- ExaML version 3 has been developed as a high-performance tool for inferring phylogenies from large datasets, including whole-transcriptome and whole-genome alignments, utilizing supercomputers.
- The latest version introduces enhancements like new substitution models, a novel load balance algorithm for better performance, and is optimized for Intel MIC-based hardware platforms.
Article Abstract
Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. We present ExaML version 3, a dedicated production-level code for inferring phylogenies on whole-transcriptome and whole-genome alignments using supercomputers.
Results: We introduce several improvements and extensions to ExaML: Extensions of substitution models and supported data types, the integration of a novel load balance algorithm as well as a parallel I/O optimization that significantly improve parallel efficiency, and a production-level implementation for Intel MIC-based hardware platforms.
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Source |
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4514929 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btv184 | DOI Listing |
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