CCD 1.0 – Core Collection of Diverse Taxa

CCD 1.0

:: DESCRIPTION

CCD is a Java software package for the selection of core collections of diverse taxa (e.g. from germplasm collections) that are intended to capture the genetic diversity of the input dataset.

::DEVELOPER

The UEA Computational Biology Laboratory at the University of East Anglia (UEA)

:: SCREENSHOTS

CCD

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java

:: DOWNLOAD

  CCD

:: MORE INFORMATION

Citation

Davey R, Savva G, Jing R, Lott M, Ellis THN, Ambrose M, Moulton V, Flavell A, Roberts I and Dicks J (2006)
Germplasm collections: Gaining new knowledge from old datasets.
Proceedings of the 2nd UK KDD Conference pp 32-38.

FuseNet – Gene Network Inference by Fusing data from Diverse Distributions

FuseNet

:: DESCRIPTION

FuseNet is a Markov network formulation that infers networks from a collection of nonidentically distributed datasets.

::DEVELOPER

FuseNet team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 FuseNet

:: MORE INFORMATION

Citation

Gene network inference by fusing data from diverse distributions.
Žitnik M, Zupan B.
Bioinformatics. 2015 Jun 15;31(12):i230-i239. doi: 10.1093/bioinformatics/btv258.

cMonkey 2 – Biclustering from Diverse System Biology Data

cMonkey 2

:: DESCRIPTION

cMonkey identifies relevant conditions in which the genes within a given bicluster (where “biclustering” is condition- or cell-state-specific clustering) are expected to be co-regulated (importantly, in later stages of analysis we use only these conditions to learn TFs and EFs that influence each bicluster). The methods separates the calculation of the score components associated with each datatype into individual calculations but still effectively sample biclusters that optimally satisfy multiple model components (each representing a separate data-type). The method was designed as a preprocessing step for network inference and performed well in comparison to all other methods tested when the trade-off between sensitivity, specificity, and coverage (fraction of conditions and genes included in one or more biclusters) were considered, particularly in context of the other bulk characteristics (cluster size, residual, etc.).

::DEVELOPER

the Bonneau Lab , Baliga Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

cMonkey

:: MORE INFORMATION

Citation

cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism.
Reiss DJ, Plaisier CL, Wu WJ, Baliga NS.
Nucleic Acids Res. 2015 Apr 14. pii: gkv300.

BMC Bioinformatics. 2006 Jun 2;7:280.
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks.
Reiss DJ, Baliga NS, Bonneau R.

AV454 1.0 – de novo Consensus Assembler designed for reads derived from diverse Viral Populations

AV454 1.0

:: DESCRIPTION

AV454 (AssembleViral454) is an assembler, based on the ARACHNE package, designed for small and non-repetitive genomes sequenced at high depth. It was specifically designed to assemble read data generated from a mixed population of viral genomes. Reads need not be paired, and it is assumed that no sequence repeat in the genome would be large enough to fully contain an average read.

::DEVELOPER

Computational R&D, The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 AV454

:: MORE INFORMATION