NEIGHBOR

NEIGHBOR. This program implements the Neighbor-Joining method of Saitou and Nei (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. Part of Phylip.

© Copyright 1991-2006 by the University of Washington. Written by Joseph Felsenstein. Edited by NGBW team.

Manual: http://evolution.genetics.washington.edu/phylip/doc/dnadist.html

INPUT = DNA distance matrix

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 3.66       
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