


WEIGHBOR(L)                                           WEIGHBOR(L)


NAME
       weighbor - weighted neighbor joining

SYNOPSIS
       weighbor  [-L  sequenceLength] [-b alphabetSize] [-i file
       Name] [-o fileName] [-v[v[v]]] [-V]

DESCRIPTION
       Weighbor takes an input  file  of  pairwise  distances  in
       Phylip  format  (see  section FILE FORMATS below) and com
       putes the phylogentic tree that best corresponds to  those
       distances.  The  output  is  the  tree  in  the  lisp-like
       'Newick' format. Currently the input is  read  from  stdin
       and the output is written to stdout.  Note, several inputs
       can be sent to weighbor and it will process each in  order
       and  print the corresponding tree.  Additional information
       about how the tree was built can be output to a  log  file
       (currently weighbor.out ). The amount of information writ
       ten to the log file can be controlled.

       These options are available:

       -L sequenceLength
              Sets the length of the sequences. Default  is  500.
              This  is the effective sequence length equal to the
              number of varying sites.  Note if the -L option  is
              not used then the program will print a warning mes
              sage to stderr indicating that  it  is  using  this
              default length.

       -b alphabetSize
              Sets the size of the alphabet of characters (number
              of bases) b.  1/b is equal to the  probablity  that
              there  will be a match for infinite evolution time.
              The default value for b is 4.

       -i fileName
              Read input from the filename given. Default  is  to
              read from stdin.

       -o fileName
              Write output to the given file. Default is to write
              to stdout.

       -v     Turns on logging and  creates  the  logfile  weigh
              bor.out  The  amount of information can be adjusted
              by using -v, -vv or -vvv to get progressively  more
              detailed  information  in the logfile. At level one
              (-v) the the logfile will contain the pair of  taxa
              that  was joined at each iteration of the algorithm
              along with the taxon that was the next best choice.
              Also printed is the p-value of this triplet.

       -V     Print out the version number.



Ver 1.2                    [16-Jun-01]                          1





WEIGHBOR(L)                                           WEIGHBOR(L)


FILE FORMATS
       Weighbor tries to be as flexable as possible in the format
       of the input file it will allow, while maintaining  PHYLIP
       compatibility.  A file that conforms EXACTLY to the PHYLIP
       format (as defined in the PHYLIP package) will  work  with
       PROVIDED  the  first character after the 10-character name
       (i.e., the 11th character on the line) is a space  ('  '),
       tab or newline.

       Additionally we have added the following extensions.

       Long taxon names.
              Taxon names can be up to 128 characters long. There
              is one caveat, spaces embedded in the file name can
              only  exist from position 2-9. A space before pos 2
              will be discared and after position 9  will  termi
              nate the name. Any non-white space character can be
              used in the name.


       Tab and newline delimiters
              Weighbor will  allow  both  tabs  and  newlines  to
              delimit  taxon  names so the following will be read
              correct even though it is not a valid PHYLIP format
              because  the names are not padded to 10 characters.

       3
       Name1
       0 1 2
       Name2
       1 0 2
       Name3
       1 2 0



       Lower triangular form
              Weighbor will also a  distance  matrices  in  lower
              triangular  form.  For example the following matrix
              will result in the same distance matrix as the pre
              vious sample

       3
       Name1
       0
       Name2
       1 0
       Name3
       1 2 0



       Symmetry sanity checks
              Weigbhor  will  force  symmetry  on  non  symmetric



Ver 1.2                    [16-Jun-01]                          2





WEIGHBOR(L)                                           WEIGHBOR(L)


              inputs. It does so by  averaging  the  given  input
              with its transpose.


DEVELOPMENT TEAM
       W. Bruno <wjb@dnamining.com>

       A. Halpern <halpern@ender.unm.edu>

       N. D. Socci <soccin@rockefeller.edu>















































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