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.

                                                                                  ANALYSEDISTS(1)