NoDe – Error-correcting Algorithm for 454 Pyrosequencing Reads

NoDe

:: DESCRIPTION

NoDe (Noise Detector) is a new error correction algorithm which was trained to identify those positions in 454 sequencing reads that are likely to have an error, and subsequently clusters those error-prone reads with correct reads resulting in error-free representative read.

::DEVELOPER

The Bioinformatics team of the Microbiology Unit, SCK.CEN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

NoDe

:: MORE INFORMATION

Citation:

NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads.
Mysara M, Leys N, Raes J, Monsieurs P.
BMC Bioinformatics. 2015 Mar 15;16(1):88.

setsApp 2.2.0 – Save and Manipulate Sets of Nodes and Edges

setsApp 2.2.0

:: DESCRIPTION

SetsApp is a Cytoscape 3 app allowing the user to create and manipulate sets of nodes or edges (but not sets with both nodes and edges, at least in the current version) in Cytoscape. Sets can be created for different networks.

::DEVELOPER

setsApp team

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux/MacOsX
Java
Cytoscape

:: DOWNLOAD

SetsApp

:: MORE INFORMATION

Citation

setsApp: Set operations for Cytoscape Nodes and Edges.
Morris JH, Wu A, Doncheva NT, Albrecht M, Ferrin TE.
F1000Res. 2014 Jul 1;3:149. doi: 10.12688/f1000research.4392.1.

CyToStruct 0.2.5.2 – Launching Arbitrary External Apps (such as Viewers) for Nodes/Edges

CyToStruct 0.2.5.2

:: DESCRIPTION

CyToStruct is a Cytoscape app for executing external applications in command or batch mode. CyToStruct allows the user to define simple yet expressive rules for executing external applications by clicking on a context menu of a node/edge.

::DEVELOPER

Rachel Kolodny

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux/ MacOsX
Java
Cytoscape

:: DOWNLOAD

CyToStruct

:: MORE INFORMATION

Citation:

CyToStruct: Augmenting the Network Visualization of Cytoscape with the Power of Molecular Viewers.
Nepomnyachiy S, Ben-Tal N, Kolodny R.
Structure. 2015 Apr 3. pii: S0969-2126(15)00076-3. doi: 10.1016/j.str.2015.02.013

dendsort 0.2 – Optimize Ordering of Nodes in a Dendrogram

dendsort 0.2

:: DESCRIPTION

dendsort includes functions to optimize ordering of nodes in a dendrogram, without affecting the meaning of the dengrogram. A dengrogram can be sorted based on the average distance of subtrees, or based on the smallest distance value. These sorting methods improve readability and interpretability of tree structure, especially for tasks such as comparison of different disntance measures or linkage types and identification of tight clusters and outliers. As a result, it also introduces more meaningful reordering for a coupled heatmap visualization.

::DEVELOPER

Bioinformatics Research Group, Belgium

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / WIndows / MacOsX
R package

:: DOWNLOAD

dendsort

:: MORE INFORMATION

Phyrex 1.1 – Reconstruction of Continuous Character Trait Values at nodes of Phylogenetic Trees

Phyrex 1.1

:: DESCRIPTION

Phyrex (PHYlogenetic REconstruction by use of gene eXpression and alternate mRNA splicing patterns) is a program for reconstructing ancestral gene expression profiles and sequence data on a given phylogenetic tree. The program uses a Minimum Evolution algorithm to reconstruct the gene expression profiles and a combination of BaseML and ClustalW to reconstruct the ancestral sequences.

::DEVELOPER

Roald Rossnes

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux/MacOsX
Java
C++ Compiler

:: DOWNLOAD

Phyrex

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2005 May 27;6:127.
Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.
Rossnes R, Eidhammer I, Liberles DA.