AnalyseDists − Analyse a distance matrix
reads a distance matrix (given as lower triangle matrix)
from stdin and writes a split decomposition and a cluster
analysis of this distance matrix to stdout. The line before
the distance matrix must be of the form
> Y x [comments]
where ’x’ gives the number of taxa, ’Y’ is a single character that indicates the type of distance and ’comment’ is an arbitrary comment. This matches the output format of, e.g., RNAdistance. The input data file may contain arbitrary lines before and after the distance matrix. All lines beginning with ’> ’ that are not of the above form are written to stdout. The program continues reading until it encounters an EOF condition or the terminator character ’@’.
A list of taxa names can be specified in the input stream. The list must begin with a line of the form
if fname is present, it will be used to name the postscript output files. The entries have the form ’x : Taxon’, where x is the number of taxon, i.e., the corresponding row and column of the distance matrix. The taxa list need not be complete. It must end however with a line beginning with ’*’ or any of the separator characters. The taxa list is printed on top of the output.
specifies the analysis methods to be used.
Cluster analysis using Ward’s method. A PostScript file named ’[fname_]wards.ps’ is created containing a drawing of the tree.
Cluster analysis using Saitou’s neighbour joining method. A PostScript file named ’[fname_]nj.ps’ is created containing a drawing of the tree.
The method of
split decomposition was proposed by H.J. Bandelt and A.W.M.
Dress (Adv Math, 92:1992,47).
The variance method for cluster analysis is due to H.J. Ward. (J Amer Stat Ass, 58:1963,236).
The neighbour joining method was published by Saitou and Nei (Mol Biol Evol, 4:1987,406).
This program is part of the Vienna RNA Package.
This a beta test version.
This man page is part of the Vienna RNA Package version 1.2
Peter F Stadler and Ivo L Hofacker.
Comments should be sent to email@example.com.