:: DESCRIPTION
qPMS9 is a parallel exact qPMS (quorum Planted Motif Search) algorithm that offers significant runtime improvements on DNA and protein datasets
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
qPMS9: an efficient algorithm for quorum Planted Motif Search.
Nicolae M, Rajasekaran S.
Sci Rep. 2015 Jan 15;5:7813. doi: 10.1038/srep07813.
:: DESCRIPTION
SwiftLink performs multipoint parametric linkage analysis on large consanguineous pedigrees and is primarily targeted at pedigrees that cannot be analysed by a Lander-Green algorithm based program, i.e. many markers, but larger pedigrees.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2013 Feb 15;29(4):413-9. doi: 10.1093/bioinformatics/bts704. Epub 2012 Dec 13.
SwiftLink: parallel MCMC linkage analysis using multicore CPU and GPU.
Medlar A1, Głowacka D, Stanescu H, Bryson K, Kleta R.
:: DESCRIPTION
ParaAT (Parallel Alignment and back-Translation) is a parallel tool that parallelly constructs protein-coding DNA alignments for a large number of homologs. ParaAT is well suited for large-scale data analysis in the high-throughput era, providing good scalability and exhibiting high parallel efficiency for computationally demanding tasks.
::DEVELOPER
The National Genomics Data Center (NGDC)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Biochem Biophys Res Commun. 2012 Mar 23;419(4):779-81. Epub 2012 Feb 27.
ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments.
Zhang Z, Xiao J, Wu J, Zhang H, Liu G, Wang X, Dai L.
:: DESCRIPTION
ParaBWT is a new and practical parallelized Burrows-Wheeler transform (BWT) and suffix array construction algorithm for big genome data, which has a linear space complexity with a small constant factor.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Liu Y, Hankeln T, Schmidt B.
Parallel and Space-Efficient Construction of Burrows-Wheeler Transform and Suffix Array for Big Genome Data.
IEEE/ACM Trans Comput Biol Bioinform. 2016 May-Jun;13(3):592-8. doi: 10.1109/TCBB.2015.2430314. PMID: 27295644.
:: DESCRIPTION
MSAProbs is a new and practical multiple alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior probabilities. Assessed using the popular benchmarks: BAliBASE, PREFAB, SABmark and OXBENCH, MSAProbs achieves statistically significant accuracy improvements over the existing top performing aligners, including ClustalW, MAFFT, MUSCLE, ProbCons and Probalign. Furthermore, MSAProbs is optimized for multi-core CPUs by employing a multi-threaded design, leading to a competitive execution time compared to other aligners.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Yongchao Liu, Bertil Schmidt, Douglas L. Maskell:
“MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities“.
Bioinformatics, 2010, 26(16): 1958 -1964
:: DESCRIPTION
CUDASW++ (compute unified device architecture) is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Yongchao Liu, Bertil Schmidt, Douglas L. Maskell:
“CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions“.
BMC Research Notes, 2010, 3:93
:: DESCRIPTION
PEANUT is a read mapper for DNA or RNA sequence reads. Read mapping is the process of aligning biological DNA or RNA sequencing reads to a known reference genome.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Köster J, Rahmann S (2014).
Massively parallel read mapping on GPUs with the q-group index and PEANUT.
PeerJ 2:e606 http://dx.doi.org/10.7717/peerj.606
:: DESCRIPTION
RPMCMC is a parallel MCMC algorithm for discovering diverse motifs from large sequence sets
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Repulsive parallel MCMC algorithm for discovering diverse motifs from large sequence sets.
Ikebata H, Yoshida R.
Bioinformatics. 2015 Jan 11. pii: btv017
:: DESCRIPTION
The smallWig tool provides compression/decompression for WIG files.
::DEVELOPER
Zhiying Wang, Tsachy (Itschak) Weissman
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
smallWig: Parallel Compression of RNA-seq WIG Files.
Wang Z, Weissman T, Milenkovic O.
Bioinformatics. 2015 Sep 30. pii: btv561.
:: DESCRIPTION
ERA (Elastic Range), a disk-based suffix tree construction method, which works efficiently with very long strings that are much larger than the available memory.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Essam Mansour, Amin Allam, Spiros Skiadopoulos, Panos Kalnis:
ERA: Efficient Serial and Parallel Suffix Tree Construction for Very Long Strings.
PVLDB 5(1): 49-60 (2011)
