SEED 1.5.1 – Clustering Next Generation Sequences

SEED 1.5.1

:: DESCRIPTION

SEED is a software for clustering large sets of Next Generation Sequences (NGS) with hundreds of millions of reads in a time and memory efficient manner. Its algorithm joins highly similar sequences into clusters that can differ by up to three mismatches and three overhanging residues.

::DEVELOPER

Girke Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ MacOsX/Windows

:: DOWNLOAD

 SEED

:: MORE INFORMATION

Citation

SEED: efficient clustering of next-generation sequences.
Bao E, Jiang T, Kaloshian I, Girke T.
Bioinformatics. 2011 Sep 15;27(18):2502-9. doi: 10.1093/bioinformatics/btr447. Epub 2011 Aug 2.

PyWATER 1.0 – Find Conserved Water Molecules in Proteins by clustering

PyWATER 1.0

:: DESCRIPTION

PyWATER is a PyMOL plugin to find conserved water molecules in X-ray protein structure.

::DEVELOPER

PyWATER team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOs
  • Python
  • PyMOL

:: DOWNLOAD

 PyWATER

:: MORE INFORMATION

Citation

PyWATER: A PyMOL plugin to find conserved water molecules in proteins by clustering.
Patel H, Grüning BA, Günther S, Merfort I.
Bioinformatics. 2014 Jul 1. pii: btu424

M-pick – Modularity-based Clustering method for OTU picking

M-pick

:: DESCRIPTION

M-pick is a modularity-based clustering method for OTU picking

::DEVELOPER

Xiaoyu Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 M-pick

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Feb 7;14:43. doi: 10.1186/1471-2105-14-43.
M-pick, a modularity-based method for OTU picking of 16S rRNA sequences.
Wang X1, Yao J, Sun Y, Mai V.

TreqCG 0.3 – Clustering Accelerates High-Throughput Sequencing Read Mapping

TreqCG 0.3

:: DESCRIPTION

TreqCG is a method to accelerate and improve read mapping based on an initial clustering of up to billions of high-throughput sequencing reads yielding clusters of high stringency and a high degree of overlap.

::DEVELOPER

Schliep lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD

 TreqCG

:: MORE INFORMATION

Citation

Mahmud, Md and Schliep, Alexander.
TreQ-CG: Clustering Accelerates High-Throughput Sequencing Read Mapping (2014)

QCanvas 1.2.1 – Fast Clustering and Visualization of data

QCanvas 1.2.1

:: DESCRIPTION

QCanvas integrates diverse clustering algorithms and an interactive heatmap display interface. It directly imports raw experimental data in a matrix format and displays these data in a heatmap.

::DEVELOPER

Lab of Bioinformatics and Molecular Design

:: SCREENSHOTS

Qcanvas

:: REQUIREMENTS

  • Windows
  • Java

:: DOWNLOAD

 QCanvas

:: MORE INFORMATION

Citation

Genomics Inform. 2012 Dec;10(4):263-5. doi: 10.5808/GI.2012.10.4.263.
QCanvas: An Advanced Tool for Data Clustering and Visualization of Genomics Data.
Kim N, Park H, He N, Lee HY, Yoon S.

AptaCluster / AptaGUI – Efficient Clustering of HT-SELEX Aptamer Pools

AptaCluster / AptaGUI

:: DESCRIPTION

AptaCluster allows for an efficient clustering of whole HT-SELEX aptamer pools; a task that could not be accomplished with traditional clustering algorithms due to the enormous size of such datasets

AptaGUI is a graphical user interface for AptaCluster, written in Java. This program allows for visual inspection of HT-SELEX experiments in a concise and efficient manner.

::DEVELOPER

Teresa Przytycka Research Group

:: SCREENSHOTS

AptaGUI

:: REQUIREMENTS

  • Windows/Linux / MacOsX
  • Java

:: DOWNLOAD

 AptaCluster / AptaGUI

:: MORE INFORMATION

Citation:

AptaCluster – A Method to Cluster HT-SELEX Aptamer Pools and Lessons from Its Application.
Hoinka J, Berezhnoy A, Sauna ZE, Gilboa E, Przytycka TM.
Research in Computational Molecular Biology Lecture Notes in Computer Science Volume 8394, 2014, pp 115-128

MS-Cluster 20110327 – Clustering Millions of Tandem Mass Spectra

MS-Cluster 20110327

:: DESCRIPTION

MS-Cluster is a software of clustering of MS/MS spectra takes advantage of this redundancy by identifying multiple spectra of the same peptide and replacing them with a single representative spectrum. Analyzing only representative spectra results in significant speed-up of MS/MS database searches. The new version of MSCluster also supports the creation of spectral archives.

::DEVELOPER

Ari Frank , CCMS The Center for Computational Mass Spectrometry

:: REQUIREMENTS

  • Linux/windows
  • java

:: DOWNLOAD

 MS-Cluster

:: MORE INFORMATION

Citation:

Clustering Millions of Tandem Mass Spectra.
Ari M. Frank, Nuno Bandeira, Zhouxin Shen, Stephen Tanner, Steven P. Briggs, Richard D. Smith and Pavel A. Pevzner.
To appear in J. of Proteome Research, 2007.

CLOSET r78 – CLoud Open SequencE clusTering

CLOSET r78

:: DESCRIPTION

CLOSET is a map-reduce framework for clustering sequences from metagenomic samples, such as 454 reads.

::DEVELOPER

Prof. Srinivas Aluru Research group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
  • HADOOP cluster

:: DOWNLOAD

  CLOSET

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2013 Feb;11(1):1340001. doi: 10.1142/S0219720013400015. Epub 2012 Dec 25.
Large-scale metagenomic sequence clustering on map-reduce clusters.
Yang X1, Zola J, Aluru S.

ClusterEnG – Interactive Education in Clustering

ClusterEnG

:: DESCRIPTION

ClusterEnG (acronym for Clustering Engine for Genomics) is an educational web resource on clustering and visualization of high-dimensional datasets. The resource currently offers visualization of PCA, t-SNE vectors of input dataset for several clustering algorithms. Furthermore, the user can also explore eighteen internal clustering validation measures to compare different clustering results.

::DEVELOPER

Jun S. Song’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

ClusterEnG

:: MORE INFORMATION

Citation

Manjunath M, Zhang Y, Yeo SH, Sobh O, Russell N, Followell C, Bushell C, Ravaioli U, Song JS.
ClusterEnG: an interactive educational web resource for clustering and visualizing high-dimensional data.
PeerJ Comput Sci. 2018;4:e155. doi: 10.7717/peerj-cs.155. Epub 2018 May 21. PMID: 30906871; PMCID: PMC6429934.