:: DESCRIPTION
birgHPCC (Bioinformatic Research Group High Performance CUDA Computing) is a free Linux Live DVD distribution based on PelicanHPC and birgHPC.birgHPCC is capable of creating and configuring a compute unified device architecture (CUDA) computing cluster, hence the extra “C” in the name.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
CUSHAW3 (the third distribution of CUSHAW software package for next-generation sequencing read alignment) is an open-source parallelized, sensitive and accurate short-read aligner.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Parallel and Scalable Short-Read Alignment on Multi-Core Clusters Using UPC+.
González-Domínguez J, Liu Y, Schmidt B.
PLoS One. 2016 Jan 5;11(1):e0145490. doi: 10.1371/journal.pone.0145490.
PLoS One. 2014 Jan 22;9(1):e86869. doi: 10.1371/journal.pone.0086869. eCollection 2014.
CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding.
Liu Y1, Popp B2, Schmidt B1.
:: DESCRIPTION
TFM-CUDA is a CUDA implementation of parallel algorithms able to:
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation
Mathieu Giraud and Jean-Stéphane Varré,
Parallel Position Weight Matrices Algorithms,
Parallel Computing, 10.1016/j.parco.2010.10.001
:: DESCRIPTION
CLAST (CUDA implemented large-scale alignment search tool) is a tool that enables analyses of millions of reads and thousands of reference genome sequences, and runs on NVIDIA Fermi architecture graphics processing units.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
CLAST: CUDA implemented large-scale alignment search tool.
Yano M, Mori H, Akiyama Y, Yamada T, Kurokawa K.
BMC Bioinformatics. 2014 Dec 11;15:406. doi: 10.1186/s12859-014-0406-y.
:: DESCRIPTION
GPU3SNP is a multi-GPU tool that exhaustively analyzes case-control datasets looking for 3-SNP combinations that present epistatic interaction.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
SWCuda (SmithWaterman-CUDA)allows to perform alignments between one or more sequences and a database (all the sequences, even in the DB, are intended to be proteinic). It is implemented in the recently released CUDA programming environment by NVidia.
::DEVELOPER
Svetlin A. Manavski, Giorgio Valle,
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Svetlin A. Manavski, Giorgio Valle,
“CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment“,
BMC Bioinformatics 2008, 9(Suppl 2):S10 (26 March 2008)
:: DESCRIPTION
cuda-sim is a python package providing CUDA GPU accelerated biochemical network simulation
::DEVELOPER
Yanxiang Zhou and Chris Barnes, the Theoretical Systems Biology group at Imperial College London
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
“GPU accelerated biochemical network simulation.”
Y. Zhou, J. Liepe, X. Sheng, M.P.H. Stumpf, C. Barnes
Bioinformatics. 2011 Mar 15;27(6):874-6.
:: DESCRIPTION
CUDA-BLASTP is designed to accelerate NCBI BLAST for scanning protein sequence databases by taking advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs. CUDA-BLASTP also has a utility to convert FASTA format database into files readable by CUDA-BLASTP.
::DEVELOPER
Parallel and Distributed Architectures
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Weiguo Liu, Bertil Schmidt, Wolfgang Müller-Wittig:
“CUDA-BLASTP: accelerating BLASTP on CUDA-enabled graphics hardware“.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2011, 8(6): 1678-1684
:: DESCRIPTION
GPUFRAGFOLD is a CUDA ACELERATED Protein Structure Prediction Tool.
:DEVELOPER
Bioinformatics Group – University College London
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
