:: DESCRIPTION
PBOOST is a GPU based tool for parallel permutation tests in genome-wide association studies.
::DEVELOPER
Laboratory for Bioinformatics and Computational Biology, HKUST
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
PBOOST: a GPU-based tool for parallel permutation tests in genome-wide association studies.
Yang G, Jiang W, Yang Q, Yu W.
Bioinformatics. 2014 Dec 21. pii: btu840.
:: 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)
:: DESCRIPTION
ACME (Advanced parallel motif extractor) is an advanced parallel motif extractor. ACME arranges the search space in contiguous blocks that take advantage of the cache hierarchy in modern architectures, and achieves almost an order of magnitude performance gain in serial execution.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Majed Sahli, Essam Mansour, Panos Kalnis:
ACME: Efficient Parallel Motif Extraction from Very Long Sequences.
Technical Report
:: DESCRIPTION
GRAPES is a querying system for parallel searching in databases of graphs, and single target graph, using symmetric multiprocessing (SMP) architectures. It implements a parallel version of well established graph searching algorithms providing efficient solutions for graphs indexing and matching.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
GRAPES: a software for parallel searching on biological graphs targeting multi-core architectures.
Giugno R, Bonnici V, Bombieri N, Pulvirenti A, Ferro A, Shasha D.
PLoS One. 2013 Oct 22;8(10):e76911. doi: 10.1371/journal.pone.0076911.
:: DESCRIPTION
Parallel-QC is a fast computational engine specifically designed for general NGS data QC. Parallel-QC can complete sequencing-quality assessment accuracy and efficiency. Possible contaminating species could also be identified without any prior information. And the whole processing of Parallel-QC is quite fast since it is optimized based on parallel computation.
::DEVELOPER
Bioinformatics Group , Single-cell Reseearch Center of Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences (QIBEBT-CAS).
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2013;8(4):e60234. doi: 10.1371/journal.pone.0060234. Epub 2013 Apr 2.
QC-Chain: fast and holistic quality control method for next-generation sequencing data.
Zhou Q1, Su X, Wang A, Xu J, Ning K.
:: DESCRIPTION
GHOST-MP is a parallel sequence similarity search tool. It searches for similar sequences among nucleotide query sequences and amino acid sequence database like BLASTX.
::DEVELOPER
Akiyama Laboratory , Tokyo Institute of Technology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Int J Mol Sci. 2017 Oct 11;18(10). pii: E2124. doi: 10.3390/ijms18102124.
A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data.
Kakuta M, Suzuki S, Izawa K, Ishida T, Akiyama Y
:: DESCRIPTION
RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein’s dnaml which is part of the PHYLIP package.
RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. RAxML-NG is a successor of RAxML (Stamatakis 2014) and leverages the highly optimized likelihood computation implemented in libpll (Flouri et al. 2014).
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2019 Nov 1;35(21):4453-4455. doi: 10.1093/bioinformatics/btz305.
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference.
Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A
Bioinformatics. 2014 May 1;30(9):1312-3. doi: 10.1093/bioinformatics/btu033. Epub 2014 Jan 21.
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
Stamatakis A.
S.A. Berger, D. Krompaß, A. Stamatakis:
“Performance, Accuracy and Web-Server for Evolutionary Placement of Short Sequence Reads under maximum-likelihood“.
Systematic Biology 60(3):291-302, 2011.
:: DESCRIPTION
parSRA is a framework to execute short read aligners on compute clusters.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
ParDRe is a de novo parallel tool to remove duplicated and near-duplicated reads through the clustering of Single-End or Paired-End sequences from fasta or fastq files.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
ParDRe: Faster Parallel Duplicated Reads Removal Tool for Sequencing Studies.
González-Domínguez J, Schmidt B.
Bioinformatics. 2016 Jan 22. pii: btw038.
:: DESCRIPTION
ABySS (Assembly By Short Sequences) is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I.
ABySS: A parallel assembler for short read sequence data.
Genome Res. 2009. 19: 1117-1123
