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

SolubiS 1.0 – Optimize your protein

SolubiS 1.0

:: DESCRIPTION

SolubiS is a method to identify stabilizing mutations that reduce the aggregation tendency of a protein.

The Solubis plugin for YASARA is a software package to identify mutants that decrease the aggregation tendency with YASARA. This package combines TANGO, FoldX and YASARA.

::DEVELOPER

Switch Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Mac / Linux
YASARA

:: DOWNLOAD

Solubis

:: MORE INFORMATION

Citation

Solubis: a webserver to reduce protein aggregation through mutation.
Van Durme J, De Baets G, Van Der Kant R, Ramakers M, Ganesan A, Wilkinson H, Gallardo R, Rousseau F, Schymkowitz J.
Protein Eng Des Sel. 2016 Jun 9. pii: gzw019.

Solubis: Optimize your protein.
De Baets G, Van Durme J, van der Kant R, Schymkowitz J, Rousseau F.
Bioinformatics. 2015 Mar 19. pii: btv162.

Rseg 1.0 – an R package to Optimize Segmentation of SNP array data

Rseg 1.0

:: DESCRIPTION

Rseg allows the user to define sample-specific thresholds to call gains and losses in an interactive way. It also allows the user to correct for RMA induced normalization artifacts in case of imbalance between losses and gains.

::DEVELOPER

Lamy P (plamy@cs.au.dk), Wiuf C, Ørntoft TF, Andersen CL.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux / MacOsX
R package

:: DOWNLOAD

Rseg

:: MORE INFORMATION

Citation

Rseg–an R package to optimize segmentation of SNP array data.
Lamy P, Wiuf C, Ørntoft TF, Andersen CL.
Bioinformatics. 2011 Feb 1;27(3):419-20.

GAPWM 1.0 – Genetic Algorithm Method for Optimizing a Position Weight Matrix

GAPWM 1.0

:: DESCRIPTION

GAPWM (Genetic Algorithm Method for Optimizing a Position Weight Matrix) implements a simple method to improve a poorly estimated PWM using chromatin

::DEVELOPER

Leping Li, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

GAPWM

:: MORE INFORMATION

Citation:

Li, L., Liang, Y., and Bass, R.L.
GAPWM: a genetic algorithm method for optimizing a position weight matrix.
Bioinformatics, 2007, 23, 1188-1194.