Name
Abstract | ||
|---|---|---|
CodeML (part of the PAML package) implements a maximum likelihood-based approach to detect positive selection on a specific branch of a given phylogenetic tree. While CodeML is widely used, it is very compute-intensive. We present SlimCodeML, an optimized version of CodeML for the branch-site model. Our performance analysis shows that SlimCodeML substantially outperforms CodeML (up to 9.38 times faster), especially for large-scale genomic analyses. |
Year | DOI | Venue |
|---|---|---|
2012 | 10.1109/IPDPSW.2012.88 | Parallel and Distributed Processing Symposium Workshops & PhD Forum |
Keywords | Field | DocType |
performance analysis,positive selection,optimized version,branch-site model,maximum likelihood-based approach,specific branch,large-scale genomic analysis,phylogenetic tree,paml package,bioinformatics,scientific computing,phylogenetics,symmetric matrices,vectors,computational modeling,molecular evolution,maximum likelihood estimation,computing,genomics,phylogeny,matrices | Phylogenetic tree,Matrix (mathematics),Computer science,Maximum likelihood,Theoretical computer science,Symmetric matrix,Positive selection | Conference |
ISSN | ISBN | Citations |
2164-7062 | 978-1-4673-0974-5 | 4 |
PageRank | References | Authors |
0.49 | 11 | 8 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Hannes Schabauer | 1 | 27 | 3.39 |
| Mario Valle | 2 | 17 | 3.16 |
| Christoph Pacher | 3 | 19 | 6.15 |
| Heinz Stockinger | 4 | 1517 | 144.32 |
| Alexandros Stamatakis | 5 | 995 | 96.27 |
| Marc Robinson-Rechavi | 6 | 165 | 18.13 |
| Ziheng Yang | 7 | 175 | 32.68 |
| Nicolas Salamin | 8 | 20 | 4.55 |