SNPPar V1.0 – Parallel/Homoplasic SNP Finder

SNPPar V1.0

:: DESCRIPTION

SNPPar is designed to find homoplasic SNPs based on a user-defined phylogenetic tree

::DEVELOPER

SNPPar team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

SNPPar

:: MORE INFORMATION

Citation

Edwards DJ, Duchene S, Pope B, Holt KE.
SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments.
Microb Genom. 2021 Dec;7(12). doi: 10.1099/mgen.0.000694. PMID: 34874243.

PaKman – Parallel Genome Assembler for Scalable Generation of Genomic Contigs

PaKman

:: DESCRIPTION

PaKman is a scalable algorithm for generating genomic contigs on distributed memory machines.

::DEVELOPER

Ananth Kalyanaraman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

PaKman

:: MORE INFORMATION

Citation

Ghosh, Priyanka, Sriram Krishnamoorthy, and Ananth Kalyanaraman.
“PaKman: A Scalable Algorithm for Generating Genomic Contigs on Distributed Memory Machines.”
IEEE Transactions on Parallel and Distributed Systems (TPDS) vol. 32, no. 5, pp. 1191-1209, 2021. DOI: 10.1109/TPDS.2020.3043241.

pClust 1.0 – Parallel Identification of Dense Protein Clusters

pClust 1.0

:: DESCRIPTION

 PClust is a scalable parallel software for detecting dense subgraphs.

::DEVELOPER

Ananth Kalyanaraman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 pClust

:: MORE INFORMATION

Citation

C. Wu, A. Kalyanaraman.
An efficient parallel approach for identifying protein families in large-scale metagenomic data sets.
Proc. ACM/IEEE Supercomputing Conference (SC’08), Austin, TX, November 15-21. pp. 1-10. 2008

ABySS 2.3.2 – de novo, parallel, paired-end Sequence Assembler

ABySS 2.3.2

:: 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

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 ABySS

:: MORE INFORMATION

Citation

Paulino D, Warren RL, Vandervalk BP, Raymond A, Jackman SD, Birol I.
Sealer: a scalable gap-closing application for finishing draft genomes.
BMC Bioinformatics. 2015 Jul 25;16(1):230. doi: 10.1186/s12859-015-0663-4. PMID: 26209068; PMCID: PMC4515008.

Vandervalk BP, Yang C, Xue Z, Raghavan K, Chu J, Mohamadi H, Jackman SD, Chiu R, Warren RL, Birol I.
Konnector v2.0: pseudo-long reads from paired-end sequencing data.
BMC Med Genomics. 2015;8 Suppl 3(Suppl 3):S1. doi: 10.1186/1755-8794-8-S3-S1. Epub 2015 Sep 23. PMID: 26399504; PMCID: PMC4582294.

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

HECTOR 1.0 – A Parallel Homopolymer Spectrum based 454 Error Corrector

HECTOR 1.0

:: DESCRIPTION

HECTOR is a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data. In this algorithm, for the first time we have investigated a novel homopolymer spectrum based approach to handle homopolymer insertions or deletions, which are the dominant sequencing errors in 454 short-reads.

::DEVELOPER

HECTOR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HECTOR

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 May 6;15(1):131. [Epub ahead of print]
HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data.
Wirawan A, Harris RS, Liu Y, Schmidt B, Schröder J.

parastructure 0.9 – Run the Population Genetics software STRUCTURE in Parallel on a Cluster

parastructure 0.9

:: DESCRIPTION

parastructure is a perl script collection to run the population genetics software STRUCTURE in parallel on a cluster (beowulf type).

::DEVELOPER

Jacques Lagnel (lagnel@her.hcmr.gr)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 parastructure

:: MORE INFORMATION

BitPAl – Bit-parallel Alignment

BitPAl

:: DESCRIPTION

BitPAl is a bit-parallel algorithm for general, integer-scoring global alignment. Integer-scoring schemes assign integer weights for match, mismatch, and insertion/deletion.

::DEVELOPER

Laboratory for Biocomputing and Informatics at Boston University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 BitPAl

:: MORE INFORMATION

Citation

BitPAl: A Bit-Parallel, General Integer-Scoring Sequence Alignment Algorithm.
Loving J, Hernandez Y, Benson G.
Bioinformatics. 2014 Jul 29. pii: btu507.

PLAST v2.3.1 – Parallel Local Alignment Search Tool for Database Comparison

PLAST v2.3.1

:: DESCRIPTION

PLAST (Parallel Local Alignment Search Tool for Database Comparison) is an intensive bank sequence comparison with a parallel version of BLAST-like software.The algorithm exploits two key parallel features of existing and future microprocessors: the SIMD programming model (SSE instruction set) and the multithreading concept (multicore). Compared to multithreaded BLAST software, tests performed on an 8-processor server have shown speedup ranging from 3 to 6 with a similar level of accuracy.

::DEVELOPER

PLAST team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac / Linux

:: DOWNLOAD

 PLAST

:: MORE INFORMATION

Citation

V.H. Nguyen, D. Lavenier,
PLAST: parallel local alignment search tool for database comparison,
BMC Bioinformatics, 2009 10(329).

GDASC – A GPU Parallel based Server for Detecting Batch Factors

GDASC

:: DESCRIPTION

GDASC is a GPU-parallel based server used for identifying batches and classifying samples into different batches in a high dimensional gene expression dataset.

::DEVELOPER

ZHANG LAB @ NKU

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Wang X, Yi H, Wang J, Liu Z, Yin Y, Zhang H.
GDASC: a GPU parallel-based web server for detecting hidden batch factors.
Bioinformatics. 2020 Aug 15;36(14):4211-4213. doi: 10.1093/bioinformatics/btaa427. PMID: 32386292.

Parallel T-Coffee 1.914 – Parallel Multiple Sequence Aligner based on TCoffee

Parallel T-Coffee 1.914

:: DESCRIPTION

Parallel T-Coffee (PTC) is the first parallel implementation of the TCoffee multiple sequence alignment tool. It has been developed to overcome main limitations of the original method. It is based on the MPI and RMA mechanisms, and it can be run on distributed memory clusters. PTC supports a majority of options provided by TCoffee 3.79, including the 3D-Coffee mode. It can be used to align data sets consisting of hundreds of proteins in reasonable time limits.

::DEVELOPER

Prof. Srinivas Aluru Research group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler
  • Perl

:: DOWNLOAD

 Parallel T-Coffee

:: MORE INFORMATION

Citation

J. Zola, X. Yang, S. Rospondek, S. Aluru
Parallel T-Coffee: A Parallel Multiple Sequence Aligner
In Proc. of ISCA PDCS-2007, pp. 248-253, 2007.

Exit mobile version