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

DendroUPGMA 201410 – A Dendrogram Construction Utility

DendroUPGMA 201410

:: DESCRIPTION

Use DendroUPGMA to create a dendrogram from (a) a set of variables, (b) a similarity matrix or (c) a distance matrix. The program calculates a similarity matrix (only for option a), transforms similarity coefficients into distances and makes a clustering using the Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithm.

::DEVELOPER

P. Puigbo, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

S. Garcia-Vallve, J. Palau and A. Romeu (1999)
Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis.
Molecular Biology and Evolution 9:1125-1134.