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
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