NAME

       AnalyseDists - Analyse a distance matrix

SYNOPSIS

       AnalyseDists [-X[swn]]

DESCRIPTION

       AnalyseDists  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
       * [fname]
       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.

OPTIONS

       -X[swn]
              specifies the analysis methods to be used.

       [s]    Split decomposition.

       [w]    Cluster analysis using Ward's method.  A  PostScript  file  named  '[fname_]wards.ps'  is  created
              containing a drawing of the tree.

       [n]    Cluster analysis using Saitou's neighbour joining method.  A PostScript file named '[fname_]nj.ps'
              is created containing a drawing of the tree.

REFERENCES

       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.

WARNING

       This a beta test version.

VERSION

       This man page is part of the Vienna RNA Package version 1.2

AUTHOR

       Peter F Stadler and Ivo L Hofacker.

BUGS

       Comments should be sent to ivo@tbi.univie.ac.at.

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