CSC

fneighbor

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Function

Description

Algorithm

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 programs FITCH, KITSCH, and NEIGHBOR are for dealing with data which comes in the form of a matrix of pairwise distances between all pairs of taxa, such as distances based on molecular sequence data, gene frequency genetic distances, amounts of DNA hybridization, or immunological distances. In analyzing these data, distance matrix programs implicitly assume that:

• Each distance is measured independently from the others: no item of data contributes to more than one distance.
• The distance between each pair of taxa is drawn from a distribution with an expectation which is the sum of values (in effect amounts of evolution) along the tree from one tip to the other. The variance of the distribution is proportional to a power p of the expectation.

These assumptions can be traced in the least squares methods of programs FITCH and KITSCH but it is not quite so easy to see them in operation in the Neighbor-Joining method of NEIGHBOR, where the independence assumptions is less obvious.

THESE TWO ASSUMPTIONS ARE DUBIOUS IN MOST CASES: independence will not be expected to be true in most kinds of data, such as genetic distances from gene frequency data. For genetic distance data in which pure genetic drift without mutation can be assumed to be the mechanism of change CONTML may be more appropriate. However, FITCH, KITSCH, and NEIGHBOR will not give positively misleading results (they will not make a statistically inconsistent estimate) provided that additivity holds, which it will if the distance is computed from the original data by a method which corrects for reversals and parallelisms in evolution. If additivity is not expected to hold, problems are more severe. A short discussion of these matters will be found in a review article of mine (1984a). For detailed, if sometimes irrelevant, controversy see the papers by Farris (1981, 1985, 1986) and myself (1986, 1988b).

For genetic distances from gene frequencies, FITCH, KITSCH, and NEIGHBOR may be appropriate if a neutral mutation model can be assumed and Nei's genetic distance is used, or if pure drift can be assumed and either Cavalli-Sforza's chord measure or Reynolds, Weir, and Cockerham's (1983) genetic distance is used. However, in the latter case (pure drift) CONTML should be better.

Restriction site and restriction fragment data can be treated by distance matrix methods if a distance such as that of Nei and Li (1979) is used. Distances of this sort can be computed in PHYLIp by the program RESTDIST.

For nucleic acid sequences, the distances computed in DNADIST allow correction for multiple hits (in different ways) and should allow one to analyse the data under the presumption of additivity. In all of these cases independence will not be expected to hold. DNA hybridization and immunological distances may be additive and independent if transformed properly and if (and only if) the standards against which each value is measured are independent. (This is rarely exactly true).

FITCH and the Neighbor-Joining option of NEIGHBOR fit a tree which has the branch lengths unconstrained. KITSCH and the UPGMA option of NEIGHBOR, by contrast, assume that an "evolutionary clock" is valid, according to which the true branch lengths from the root of the tree to each tip are the same: the expected amount of evolution in any lineage is proportional to elapsed time.

Usage

% fneighbor 
Phylogenies from distance matrix by N-J or UPGMA method
Phylip distance matrix file: neighbor.dat
Phylip neighbor program output file [neighbor.fneighbor]: 



Cycle   4: species 1 (   0.91769) joins species 2 (   0.76891)
Cycle   3: node 1 (   0.42027) joins species 3 (   0.35793)
Cycle   2: species 6 (   0.15168) joins species 7 (   0.11752)
Cycle   1: node 1 (   0.04648) joins species 4 (   0.28469)
last cycle:
 node 1  (   0.02696) joins species 5  (   0.15393) joins node 6  (   0.03982)

Output written on file "neighbor.fneighbor"

Tree written on file "neighbor.treefile"

Done.

Go to the input files for this example
Go to the output files for this example

Command line arguments

Phylogenies from distance matrix by N-J or UPGMA method
Version: EMBOSS:6.3.0

   Standard (Mandatory) qualifiers:
  [-datafile]          distances  Phylip distance matrix file
  [-outfile]           outfile    [*.fneighbor] Phylip neighbor program output
                                  file

   Additional (Optional) qualifiers (* if not always prompted):
   -matrixtype         menu       [s] Type of data matrix (Values: s (Square);
                                  u (Upper triangular); l (Lower triangular))
   -treetype           menu       [n] Neighbor-joining or UPGMA tree (Values:
                                  n (Neighbor-joining); u (UPGMA))
*  -outgrno            integer    [0] Species number to use as outgroup
                                  (Integer 0 or more)
   -jumble             toggle     [N] Randomise input order of species
*  -seed               integer    [1] Random number seed between 1 and 32767
                                  (must be odd) (Integer from 1 to 32767)
   -replicates         boolean    [N] Subreplicates
   -[no]trout          toggle     [Y] Write out trees to tree file
*  -outtreefile        outfile    [*.fneighbor] Phylip tree output file
                                  (optional)
   -printdata          boolean    [N] Print data at start of run
   -[no]progress       boolean    [Y] Print indications of progress of run
   -[no]treeprint      boolean    [Y] Print out tree

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   "-outtreefile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Input file format

Input files for usage example

File: neighbor.dat

    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 file format

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.

Output files for usage example

File: neighbor.fneighbor

Neighbor-Joining/UPGMA method version 3.69


   7 Populations

 Neighbor-joining method

 Negative branch lengths allowed


  +---------------------------------------------Mouse     
  ! 
  !                        +---------------------Gibbon    
  1------------------------2 
  !                        !  +----------------Orang     
  !                        +--4 
  !                           ! +--------Gorilla   
  !                           +-5 
  !                             ! +--------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             4            0.04648
   4          Orang           0.28469
   4             5            0.02696
   5          Gorilla         0.15393
   5             3            0.03982
   3          Chimp           0.15168
   3          Human           0.11752
   1          Bovine          0.91769

File: neighbor.treefile

(Mouse:0.76891,(Gibbon:0.35793,(Orang:0.28469,(Gorilla:0.15393,
(Chimp:0.15168,Human:0.11752):0.03982):0.02696):0.04648):0.42027,Bovine:0.91769);

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Converted (August 2004) to an EMBASSY program by the EMBOSS team.

Target users