Name
Abstract | ||
|---|---|---|
Motivation: Due to advances in molecular sequencing and the increasingly rapid collection of molecular data, the field of phyloinformatics is transforming into a computational science. Therefore, new tools are required that can be deployed in supercomputing environments and that scale to hundreds or thousands of cores. Results: We describe RAxML-Light, a tool for large-scale phylogenetic inference on supercomputers under maximum likelihood. It implements a light-weight checkpointing mechanism, deploys 128-bit (SSE3) and 256-bit (AVX) vector intrinsics, offers two orthogonal memory saving techniques and provides a fine-grain production-level message passing interface parallelization of the likelihood function. To demonstrate scalability and robustness of the code, we inferred a phylogeny on a simulated DNA alignment (1481 taxa, 20 000 000 bp) using 672 cores. This dataset requires one terabyte of RAM to compute the likelihood score on a single tree. |
Year | DOI | Venue |
|---|---|---|
2012 | 10.1093/bioinformatics/bts309 | BIOINFORMATICS |
Keywords | Field | DocType |
computer simulation,computational biology,phylogeny | Likelihood function,Supercomputer,Terabyte,Computer science,Parallel computing,Robustness (computer science),SSE3,Message Passing Interface,Bioinformatics,Intrinsics,Scalability | Journal |
Volume | Issue | ISSN |
28 | 15 | 1367-4803 |
Citations | PageRank | References |
5 | 0.65 | 7 |
Authors | ||
6 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Alexandros Stamatakis | 1 | 995 | 96.27 |
| Andre Aberer | 2 | 40 | 6.09 |
| C Goll | 3 | 5 | 0.65 |
| S A Smith | 4 | 5 | 0.65 |
| Simon A. Berger | 5 | 71 | 7.46 |
| Fernando Izquierdo-Carrasco | 6 | 39 | 5.31 |