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    neighbor.doc

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    This file has been automatically converted from the original documentation for easy use inside the ARB help system. Differences compared with the original documentation are unintentionally caused by the conversion process. In doubt please refer to the original documentation!

     

    DOCUMENTATION

    # generated from ../../GDE/PHYLIP/doc/neighbor.html

    version 3.6
    NEIGHBOR -- Neighbor-Joining and UPGMA methods
    (C)  Copyright  1991-2000  by  the  University of Washington. Written by
    Joseph  Felsenstein.  Permission  is  granted  to  copy  this document
    provided  that no fee is charged for it and that this copyright notice
    is not removed.
    This  program implements the Neighbor-Joining method of Nei and Saitou
    (1987)  and the UPGMA method of clustering. The program was written by
    Mary  Kuhner  and  Jon  Yamato, using some code from program FITCH. An
    important  part  of the code was translated from FORTRAN code from the
    neighbor-joining  program  written by Naruya Saitou and by Li Jin, and
    is used with the kind permission of Drs. Saitou and Jin.
    NEIGHBOR  constructs  a  tree  by  successive  clustering of lineages,
    setting  branch  lengths  as  the  lineages  join.  The  tree  is  not
    rearranged thereafter. The tree does not assume an evolutionary clock,
    so  that  it  is  in  effect  an  unrooted tree. It should be somewhat
    similar  to  the tree obtained by FITCH. The program cannot evaluate a
    User  tree,  nor can it prevent branch lengths from becoming negative.
    However  the  algorithm  is far faster than FITCH or KITSCH. This will
    make it particularly effective in their place for large studies or for
    bootstrap  or  jackknife  resampling  studies  which  require  runs on
    multiple data sets.
    The  UPGMA  option  constructs  a  tree  by successive (agglomerative)
    clustering  using an average-linkage method of clustering. It has some
    relationship  to  KITSCH, in that when the tree topology turns out the
    same,  the  branch  lengths with UPGMA will turn out to be the same as
    with the P = 0 option of KITSCH.
    The  options  for  NEIGHBOR are selected through the menu, which looks
    like this:

    Neighbor-Joining/UPGMA method version 3.6a3

    Settings for this run:
      N       Neighbor-joining or UPGMA tree?  Neighbor-joining
      O                        Outgroup root?  No, use as outgroup species  1
      L         Lower-triangular data matrix?  No
      R         Upper-triangular data matrix?  No
      S                        Subreplicates?  No
      J     Randomize input order of species?  No. Use input order
      M           Analyze multiple data sets?  No
      0   Terminal type (IBM PC, ANSI, none)?  (none)
      1    Print out the data at start of run  No
      2  Print indications of progress of run  Yes
      3                        Print out tree  Yes
      4       Write out trees onto tree file?  Yes
    Y to accept these or type the letter for one to change
    Most  of  the  input  options  (L, R, S, J, and M) are as given in the
    Distance  Matrix  Programs  documentation  file,  that file, and their
    input  format  is  the same as given there. The O (Outgroup) option is
    described  in  the  main documentation file of this package. It is not
    available  when  the  UPGMA  option is selected. The Jumble option (J)
    does  not  allow  multiple jumbles (as most of the other programs that
    have  it  do),  as  there is no objective way of choosing which of the
    multiple  results  is  best,  there  being  no  explicit criterion for
    optimality of the tree.
    Option  N  chooses  between  the  Neighbor-Joining  and UPGMA methods.
    Option  S  is  the  usual  Subreplication option. Here, however, it is
    present  only  to allow NEIGHBOR to read the input data: the number of
    replicates  is  actually ignored, even though it is read in. Note that
    this  means  that  one cannot use it to have missing data in the input
    file, if NEIGHBOR is to be used.
    The  output  consists  of  an  tree  (rooted  if  UPGMA,  unrooted  if
    Neighbor-Joining)  and  the  lengths  of  the  interior  segments. The
    Average  Percent Standard Deviation is not computed or printed out. If
    the  tree  found by Neighbor is fed into FITCH as a User Tree, it will
    compute  this  quantity  if  one also selects the N option of FITCH to
    ensure that none of the branch lengths is re-estimated.
    As NEIGHBOR runs it prints out an account of the successive clustering levels, if you allow it to. This is mostly for reassurance and can be suppressed using menu option 2. In this printout of cluster levels the word "OTU" refers to a tip species, and the word "NODE" to an interior node of the resulting tree.
    The  constants  available  for  modification  at  the beginning of the
    program are "namelength" which gives the length of a species name, and
    the  usual  boolean constants that initiliaze the terminal type. There
    is  no  feature saving multiply trees tied for best, partly because we
    do not expect exact ties except in cases where the branch lengths make
    the nature of the tie obvious, as when a branch is of zero length.
    The  major advantage of NEIGHBOR is its speed: it requires a time only
    proportional   to   the  square  of  the  number  of  species.  It  is
    significantly  faster  than  version  3.5 of this program. By contrast
    FITCH  and KITSCH require a time that rises as the fourth power of the
    number  of  species.  Thus  NEIGHBOR  is  well-suited to bootstrapping
    studies  and  to  analysis of very large trees. Our simulation studies
    (Kuhner  and  Felsenstein,  1994) show that, contrary to statements in
    the  literature  by  others,  NEIGHBOR  does  not  get  as accurate an
    estimate  of  the  phylogeny  as does FITCH. However it does nearly as
    well,  and  in  view  of  its  speed  this will make it a quite useful
    program.
      _________________________________________________________________
    TEST DATA SET
        7
    Bovine      0.0000  1.6866  1.7198  1.6606  1.5243  1.6043  1.5905
    Mouse       1.6866  0.0000  1.5232  1.4841  1.4465  1.4389  1.4629
    Gibbon      1.7198  1.5232  0.0000  0.7115  0.5958  0.6179  0.5583
    Orang       1.6606  1.4841  0.7115  0.0000  0.4631  0.5061  0.4710
    Gorilla     1.5243  1.4465  0.5958  0.4631  0.0000  0.3484  0.3083
    Chimp       1.6043  1.4389  0.6179  0.5061  0.3484  0.0000  0.2692
    Human       1.5905  1.4629  0.5583  0.4710  0.3083  0.2692  0.0000
         _________________________________________________________________
    OUTPUT FROM TEST DATA SET (with all numerical options on)
    7 Populations

    Neighbor-Joining/UPGMA method version 3.6a3

    Neighbor-joining method
    Negative branch lengths allowed
    Name                       Distances
    ----                       ---------
    Bovine        0.00000   1.68660   1.71980   1.66060   1.52430   1.60430
                  1.59050
    Mouse         1.68660   0.00000   1.52320   1.48410   1.44650   1.43890
                  1.46290
    Gibbon        1.71980   1.52320   0.00000   0.71150   0.59580   0.61790
                  0.55830
    Orang         1.66060   1.48410   0.71150   0.00000   0.46310   0.50610
                  0.47100
    Gorilla       1.52430   1.44650   0.59580   0.46310   0.00000   0.34840
                  0.30830
    Chimp         1.60430   1.43890   0.61790   0.50610   0.34840   0.00000
                  0.26920
    Human         1.59050   1.46290   0.55830   0.47100   0.30830   0.26920
                  0.00000
    +---------------------------------------------Mouse
    !
    !                        +---------------------Gibbon
    1------------------------2
    !                        !  +----------------Orang
    !                        +--5
    !                           ! +--------Gorilla
    !                           +-4
    !                             ! +--------Chimp
    !                             +-3
    !                               +------Human
    !
    +------------------------------------------------------Bovine

    remember: this is an unrooted tree!

    Between        And            Length
    -------        ---            ------
       1          Mouse           0.76891
       1             2            0.42027
       2          Gibbon          0.35793
       2             5            0.04648
       5          Orang           0.28469
       5             4            0.02696
       4          Gorilla         0.15393
       4             3            0.03982
       3          Chimp           0.15167
       3          Human           0.11753
       1          Bovine          0.91769