DendroUPGMA: A dendrogram construction utility.

Created at March 2002.      
By Dr. Santi Garcia-Vallvé (santi.garcia-vallve AT urv.net) and Dr. Pere Puigbo
Biochemistry and Biotechnology Department.
Universitat Rovira i Virgili (URV). Tarragona. Spain.


Use this program 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.

For Option (a) -Construct a dendrogram from a set of variables- two input formats are available:

  • Format 1: fasta-like format - Two lines,the first one must begin with the ">" character (this will be the identifier line) and the secon one that contains the variables (separated by tabs or spaces, not a combination of both).
  • Format 2: Only one line for each set of variables (separated by spaces). The first one will be assumed to be the identifier.
For Options (b) and (c) -Construct a dendrogram from a similarity or distance matrix- the input must be a similarity or distance matrix in CSV or tab-delimited format.

Choose the input:
(a) a set of variables

Choose the coefficient used to compare between set of variables:
Pearson (r)  Jaccard (Tanimoto)   Dice  MSD   RMSD

If the Pearson coefficient (r) has been choosed, choose the transformation of r to generate the distance values (d):
d = (1 - r) * 100     d = - Ln (abs (r))

Do you want to generate 100 bootstrap replicates? No Yes

Do you want to omit rows with identical values for all the variables? No Yes

(b) a similarity matrix

Do you want to omit rows with a similarity of 1? No Yes

(c) a distance matrix

Examples:


This method of dendrogram construction has been used in the following articles:

 

If you use this server please mention its URL address and the Garcia-Vallve et al. 1999 article.


DendroUPGMA is included as external resource at the Phylogeny/evolution category from EXPASY Tools