OLYMPUS – Hybrid Clustering method in Time Series Gene Expression

HMS (hybrid motif sampler) implements a novel computational algorithm specifically designed for transcription factor binding sites (TFBS) motif discovery using ChIP-Seq data. HMS combines stochastic sampling with determinstic greedy search to achieve rapid and accurate motif pattern identification. In addition, it can identify non-ignorable inter-position dependency inside TFBS motifs.

::DEVELOPER

Ming Hu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R Package

:: DOWNLOAD

HMS

:: MORE INFORMATION

Citation

Hu M, Yu J, Taylor JM, Chinnaiyan AM, Qin ZS.
On the detection and refinement of transcription factor binding sites using ChIP-Seq data.
Nucleic Acids Res. 2010 Apr;38(7):2154-67. Epub 2010 Jan 6.

SimConcept – Hybrid approach for simplifying Composite Named Entities in Biomedical Text

SimConcept

:: DESCRIPTION

SimConcept is a hybrid approach by integrating a machine learning model with a pattern identification strategy to identify individual mentions from a composite named entity.

::DEVELOPER

SimConcept team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
Perl

:: DOWNLOAD

SimConcept

:: MORE INFORMATION

Citation

IEEE J Biomed Health Inform. 2015 Jul;19(4):1385-91. doi: 10.1109/JBHI.2015.2422651. Epub 2015 Apr 13.
SimConcept: a hybrid approach for simplifying composite named entities in biomedical text.
Wei CH, Leaman R, Lu Z.

MAXIMUS 0.2 – Hybrid Reference and de novo Assembly pipeline

MAXIMUS 0.2

:: DESCRIPTION

MAXIMUS is a genome assembly pipeline which takes the best out of multiple reference assemblies and de novo assembly. The benefits of this approach include better assembled repetitive regions, less gaps and higher accuracy for the resultant assembly.

::DEVELOPER

The Chinese University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python
Java
Pre-requisites

:: DOWNLOAD

MAXIMUS

:: MORE INFORMATION

introgress 1.23 – Mapping Components of Isolation in Hybrids

introgress 1.23

:: DESCRIPTION

introgress is a software package for mapping components of isolation in hybrids. It is an R-package that implements various methods for the analysis of gene introgression in hybrid zones.

::DEVELOPER

Buerkle lab ,University of Wyoming

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX/ Windows
R package

:: DOWNLOAD

introgress

:: MORE INFORMATION

Citation:

Molecular Ecology Resources Volume 10, Issue 2, pages 378–384, March 2010
introgress: a software package for mapping components of isolation in hybrids
ZACHARIAH GOMPERT, C. ALEX BUERKLE

Taipan 20090515 – Fast Hybrid Short-read Assembly tool

Taipan 20090515

:: DESCRIPTION

Taipan is an assembly algorithm which can be viewed as a hybrid of these two approaches. Taipan uses greedy extensions for contig construction but at each step realizes enough of the corresponding read graph to make better decisions as to how assembly should continue. We show that this approach can achieve an assembly quality at least as good as the graph-based approaches used in the popular Edena and Velvet assembly tools using a moderate amount of computing resources.

::DEVELOPER

Parallel and Distributed Architectures

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Compiler

:: DOWNLOAD

Taipan

:: MORE INFORMATION

Citation

Bertil Schmidt, Ranjan Sinha, Bryan Beresford-Smith, Simon J. Puglisi:
“A Fast Hybrid Short Read Fragment Assembly Algorithm“.
Bioinformatics, 2009, 25(17): 2279-2280

NewHybrids 1.1 Beta3 – Gibbs Sampler Estimation of Hybrid Categories

NewHybrids 1.1 Beta3

:: DESCRIPTION

NewHybrids is a program which uses the Gibbs sampler to estimate the posterior probability that genetically sampled individuals fall into each of a set of user-defined hybrid categories.

::DEVELOPER

Eric C. Anderson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows/MacOsX

:: DOWNLOAD

NewHybrids

:: MORE INFORMATION

Citation:

A model-based method for identifying species hybrids using multilocus genetic data
Eric C. Anderson and Elizabeth A. Thompson
Genetics, 160: 1217-1229. (March 2002)