For better experience, turn on JavaScript!

CUDA ClustalW

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.


Phylogeny; Sequence analysis; Nucleic acid sites, features and motifs; Nucleic acid structure analysis; Sequence sites, features and motifs


  • Operation: Multiple sequence alignment
  • Input: FASTA
  • Output: ClustalW with character counts; ClustalW; Pearson/FASTA; MSF; NEXUS; PHYLIP; SELEX; STOCKHOLM; VIENNA
  • Software interface: Commanline user interface
  • Language: C++
  • Operating system: Linux
  • License: Other
  • Cost: Free for non-commercial use
  • Version name: 1.0.0
  • Credit: -
  • Contact: Toby Gibson gibson _at_
  • Collection: Clustal


Hung CL, Lin YS, Lin CY, Chung YC, Chung YF "CUDA ClustalW: An efficient parallel algorithm for progressive multiple sequence alignment on Multi-GPUs." Comput Biol Chem. 2015 Oct;58:62-8.
PMID: 26052076

Download and documentation

If you find errors, please report here.