StructHDP 1.1 – Inference of number of Clusters and Population Structure from Admixed Genotype data.

StructHDP 1.1

:: DESCRIPTION

StructHDP is a program for automatically inferring the population structure and number of clusters from a sample of admixed genotype data. It extends the model used by Structure to allow for a potentially infinite number of populations and then chooses the number of populations that best explain the data.

::DEVELOPER

Suyash Shringarpure

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

 StructHDP

:: MORE INFORMATION

Citation

StructHDP: automatic inference of number of clusters and population structure from admixed genotype data Suyash Shringarpure;
Suyash Shringarpure ,Daegun Won; Eric P. Xing
Bioinformatics 2011 27: i324-i332

mCarts 1.2.0 – Hidden Markov model to predict Clustered RNA Motif sites

mCarts 1.2.0

:: DESCRIPTION

mCarts is a hidden Markov model (HMM)-based methods to predict clusters RNA motif sites.

::DEVELOPER

Zhang Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 mCarts

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Aug;41(14):6793-807. doi: 10.1093/nar/gkt421. Epub 2013 May 18.
Prediction of clustered RNA-binding protein motif sites in the mammalian genome.
Zhang C1, Lee KY, Swanson MS, Darnell RB.

Network Motif Clustering Toolbox 2.0 – Cluster Topological Network Motif

Network Motif Clustering Toolbox 2.0

:: DESCRIPTION

The Network Notif Clustering Toolbox is a Matlab/Octave toolbox for clustering topological network motifs in large-scale, integrated networks. The clustering algorithm is based on rigorous mathematical results and has been validated on an integrated yeast interaction network.

::DEVELOPER

Tom Michoel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Network Motif Clustering Toolbox

:: MORE INFORMATION

Citation:

Tom Michoel, Anagha Joshi,b Bruno Nachtergaelec and Yves Van de Peer
Enrichment and aggregation of topological motifs are independent organizational principles of integrated interaction networks
Mol. BioSyst., 2011,7, 2769-2778

TiCoNE 2.0.0 – Cluster multi-patient-sample Time-series data

TiCoNE 2.0.0

:: DESCRIPTION

TiCoNE (Time Course Network Enricher) is a tool for the combined analysis of time series expression data together with biological networks.It will find time patterns emerging in the expression data and check for network modules enriched with genes of similar expression behavior over time.

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java
  • Cytoscape

:: DOWNLOAD

TiCoNE

:: MORE INFORMATION

Citation

Syst Med (New Rochelle). 2019 Mar 28;2(1):1-9. doi: 10.1089/sysm.2018.0013.
Time-Resolved Systems Medicine Reveals Viral Infection-Modulating Host Targets.
Wiwie C, Kuznetsova I, Mostafa A, Rauch A, Haakonsson A, Barrio-Hernandez I, Blagoev B, Mandrup S, Schmidt HHHW, Pleschka S, Röttger R, Baumbach J

CABRA – Cluster & Annotate Blast Results Algorithm

CABRA

:: DESCRIPTION

CABRA is a web tool , which enables a rapid BLAST search in a variety of updated reference proteomes, and provides a new way to functionally evaluate the results by the subsequent clustering of the hits and annotation of the clusters.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Web Server

:: DOWNLOAD

CABRA

:: MORE INFORMATION

Citation

BMC Res Notes. 2016 Apr 30;9:253. doi: 10.1186/s13104-016-2062-y.
CABRA: Cluster and Annotate Blast Results Algorithm.
Mier P, Andrade-Navarro MA.

MCODE 1.5.1 – Cytoscape plugin that finds Clusters in a Network

MCODE 1.5.1

:: DESCRIPTION

MCODE is a Cytoscape plugin that finds clusters (highly interconnected regions) in a network. Clusters mean different things in different types of networks. For instance, clusters in a protein-protein interaction network are often protein complexes and parts of pathways, while clusters in a protein similarity network represent protein families.

::DEVELOPER

Bader Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 MCODE

:: MORE INFORMATION

Citation

Bader GD, Hogue CW.
An automated method for finding molecular complexes in large protein interaction networks.
BMC Bioinformatics. 2003 Jan 13;4(1):2.

DistMap 1.0 – A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster

DistMap 1.0

:: DESCRIPTION

DistMap is a user-friendly pipeline designed to map short reads in a MapReduce framework on a local Hadoop cluster.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Java
  • Perl
  • Mapper executable
  •  MergeSamFiles.jar and SortSam.jar from PICARD (http://picard.sourceforge.net).
  • A working Hadoop cluster.

:: DOWNLOAD

 DistMap

:: MORE INFORMATION

Citation:

Pandey RV, Schlötterer C. (2013)
DistMap: a toolkit for distributed short read mapping on a Hadoop cluster.
PLoS One. 8(8):e72614.

WordCluster – Detect Clusters of DNA Word and Genome Elements

WordCluster

:: DESCRIPTION

WordCluster is an algorithm to detect clusters of DNA words (k-mers), or any other genomic element, based on the distance between consecutive copies and an assigned statistical significance.

::DEVELOPER

The group of computational genomics and bioinformatics at Granada University (Spain)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Algorithms Mol Biol. 2011 Jan 24;6:2. doi: 10.1186/1748-7188-6-2.
WordCluster: detecting clusters of DNA words and genomic elements.
Hackenberg M, Carpena P, Bernaola-Galván P, Barturen G, Alganza AM, Oliver JL.

CAGEScan-Clustering 1.2 – Create CAGEscan Clusters from CAGE paired-end reads

CAGEScan-Clustering 1.2

:: DESCRIPTION

CAGEScan-Clustering creates transcript assemblies from CAGEScan derived Transcription Start Site (TSS) associated reads paired with randomly primed readsm, grouping them on the basis of the common location of TSS reads.

::DEVELOPER

FANTOM

:: SCREENSHOTS

N/A

: REQUIREMENTS

  • Linux
  • Perl
  • BedTools v2.9.0 or higher

:: DOWNLOAD

 CAGEScan-Clustering

:: MORE INFORMATION

Paraclu 9 – Find Clusters in Data attached to Sequences

Paraclu 9

:: DESCRIPTION

Paraclu finds clusters in data attached to sequences. It was first applied to transcription start counts in genome sequences, but it could be applied to other things too. Paraclu is intended to explore the data, imposing minimal prior assumptions, and letting the data speak for itself.

::DEVELOPER

Computational Biology Research Center[CBRC]

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 Paraclu

:: MORE INFORMATION

Citation

MC Frith, E Valen, A Krogh, Y Hayashizaki, P Carninci, A Sandelin,
A code for transcription initiation in mammalian genomes,
Genome Research 2008 18(1):1-12.