CUDA ClustalW
The multiple sequence alignment (MSA) tool, CUDA ClustalW v1.0 is a GPU version of ClustalW v2.0.1, using synchronous diagonal multiple threads and internal tasks' parallelization. The Authors report it to be able to speed up about 22 times compared to running on a single CPU.
Topic
Phylogeny;Sequence analysis;Nucleic acid sites, features and motifs;Nucleic acid structure analysis;Sequence sites, features and motifs
Detail
Operation: Multiple sequence alignment
Software interface: Commanline user interface
Language: C++
License: Other
Cost: Free for non-commercial use
Version name: 1.0.0
Credit: -
Input: FASTA
Output: ClustalW with character counts;ClustalW;Pearson/FASTA;MSF;NEXUS;PHYLIP;SELEX;STOCKHOLM;VIENNA
Contact: Toby Gibson gibson@embl.de
Collection: Clustal
Maturity: -
Publications
- CUDA ClustalW: An efficient parallel algorithm for progressive multiple sequence alignment on Multi-GPUs.
- Hung CL, et al. CUDA ClustalW: An efficient parallel algorithm for progressive multiple sequence alignment on Multi-GPUs. CUDA ClustalW: An efficient parallel algorithm for progressive multiple sequence alignment on Multi-GPUs. 2015; 58:62-8. doi: 10.1016/j.compbiolchem.2015.05.004
- https://doi.org/10.1016/j.compbiolchem.2015.05.004
- PMID: 26052076
- PMC: -
Download and documentation
Source: https://github.com/coldfunction/CUDA-clustalW/tree/master/GPU/cuda_clustalw_final
Documentation: https://github.com/coldfunction/CUDA-clustalW/blob/master/GPU/cuda_clustalw_final/README
Home page: https://github.com/coldfunction/CUDA-clustalW/tree/master/GPU/cuda_clustalw_final
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