Tag: Parallel

RAxML 8.2.12 / RAxML-NG 0.9.0- Sequential and Parallel Maximum Likelihood based inference of large phylogenetic trees

RAxML 8.2.12 / RAxML-NG 0.9.0

:: 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

the Exelixis Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  RAxML , RAxML-NG

:: 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.

ParDRe 2.2.5 – Faster Parallel Duplicated Reads Removal Tool for Sequencing Studies

ParDRe 2.2.5

:: 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

Jorge González Domínguez

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ParDRe

:: MORE INFORMATION

Citation:

ParDRe: Faster Parallel Duplicated Reads Removal Tool for Sequencing Studies.
González-Domínguez J, Schmidt B.
Bioinformatics. 2016 Jan 22. pii: btw038.

ABySS 1.9.0 – de novo, parallel, paired-end Sequence Assembler

ABySS 1.9.0

:: 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

Shaun Jackman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 ABySS

:: 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

CUDASW++ 3.1.1 – Parallel Smith Waterman Protein database search algorithm

CUDASW++ 3.1.1

:: 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

Liu, Yongchao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • CUDA toolkits and SDK 2.0 or higher.

:: DOWNLOAD

 CUDASW++

:: 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

PEANUT 1.3.7 – The ParallEl AligNment UTility

PEANUT 1.3.7

:: 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

Johannes Köster

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

  PEANUT

:: 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

smallWig – Parallel Compression of RNA-seq WIG Files

smallWig

:: DESCRIPTION

The smallWig tool provides compression/decompression for WIG files.

::DEVELOPER

Zhiying Wang, Tsachy (Itschak) Weissman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

  smallWig

:: MORE INFORMATION

Citation

smallWig: Parallel Compression of RNA-seq WIG Files.
Wang Z, Weissman T, Milenkovic O.
Bioinformatics. 2015 Sep 30. pii: btv561.

GRAPES – SMP Querying system for Efficient Parallel Subgraph Isomorphism in databases of Graphs

GRAPES 2.9

:: 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

Ferrolab @ DMI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GRAPES

:: 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.

SwiftLink – Parallel MCMC Linkage Analysis

SwiftLink

:: 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

SwiftLink team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SwiftLink

:: 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.

Ray 2.3.1 – Parallel Genome Assemblies for Parallel DNA sequencing

Ray 2.3.1

:: DESCRIPTION

Ray is a parallel software that computes de novo genome assemblies with next-generation sequencing data.

::DEVELOPER

Sébastien Boisvert

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Mac OsX/Windows
  • C++ Compiler

:: DOWNLOAD

 Ray

:: MORE INFORMATION

Citation

Genome Biol. 2012 Dec 22;13(12):R122. doi: 10.1186/gb-2012-13-12-r122.
Ray Meta: scalable de novo metagenome assembly and profiling.
Boisvert S, Raymond F, Godzaridis E, Laviolette F, Corbeil J.

Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies.
Boisvert S, Laviolette F, Corbeil J.
Journal of Computational Biology November 2010, 17(11): 1519-1533.