| ## EMBOSS: eneighbor

# Program eneighbor

## Function

Conversion of PHYLIP's neighbor

## Description

ENEIGHBOR -- Embossified Neighbor-Joining and UPGMA methods

Phylip neighbor documentation.

## Usage

Here is a sample session with eneighbor with the data:-

        5
    Alpha      0.000 1.000 2.000 3.000 3.000
    Beta       1.000 0.000 2.000 3.000 3.000
    Gamma      2.000 2.000 0.000 3.000 3.000
    Delta      3.000 3.000 3.000 0.000 1.000
    Epsilon    3.000 3.000 3.000 1.000 0.000

    % eneighbor test

    estimates phylogenies from distance matrix data using the Neighbor-Joining
    method or the UPGMA method of clustering
    Output file [eneighbor.outfile]: stdout
    Create a tree file [Y]:
    Treefile name [eneighbor.treefile]:
    Neighbor-joining [Y]:
    Outgroup root [N]:

       5 Populations

     Neighbor-joining method

     Negative branch lengths allowed

      +-------------------Gamma
      !
      !                             +---------Delta
    --3-----------------------------1
      !                             +---------Epsilon
      !
      !         +---------Alpha
      +---------2
                +---------Beta

    remember: this is an unrooted tree!

    Between        And            Length
    -------        ---            ------
       3          Gamma             1.00000
       3             1              1.50000
       1          Delta             0.50000
       1          Epsilon           0.50000
       3             2              0.50000
       2          Alpha             0.50000
       2          Beta              0.50000

    % more eneighbor.treefile
    (Gamma:1.00000,(Delta:0.50000,Epsilon:0.50000):1.50000,(Alpha:0.50000,
    Beta:0.50000):0.50000);

## Command line arguments

       Mandatory qualifiers (* if not always prompted):
      [-infile]            infile     (no help text) infile value
      [-outfile]           outfile    Output file name
      [-[no]trout]         bool       Create a tree file
    *  -treefile           outfile    Tree file name
       -[no]nj             bool       Neighbor-joining
    *  -og                 bool       Outgroup root
    *  -outgnum            integer    number of the outgroup
    *  -randseed           integer    Random number seed (must be odd)
    *  -datasets           integer    How many data sets

       Optional qualifiers:
       -[no]drawtree       bool       Draw tree
       -lt                 bool       Lower-triangular data matrix
       -ut                 bool       Upper-triangular data matrix
       -[no]sr             bool       Subreplicates
       -random             bool       Randomize input order of species
       -multsets           bool       Analyze multiple data sets
       -printdata          bool       Print out the data at start of run
       -progress           bool       Print indications of progress of run

       Advanced qualifiers: (none)

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-infile] (Parameter 1) | (no help text) infile value | Input file | Required
[-outfile] (Parameter 2) | Output file name | Output file | eneighbor.outfile
[-[no]trout] (Parameter 3) | Create a tree file | Yes/No | Yes
-treefile | Tree file name | Output file | eneighbor.treefile
-[no]nj | Neighbor-joining | Yes/No | Yes
-og | Outgroup root | Yes/No | No
-outgnum | number of the outgroup | Any integer value | 0
-randseed | Random number seed (must be odd) | Any integer value | 0
-datasets | How many data sets | Any integer value | 0
Optional qualifiers | Allowed values | Default
-[no]drawtree | Draw tree | Yes/No | Yes
-lt | Lower-triangular data matrix | Yes/No | No
-ut | Upper-triangular data matrix | Yes/No | No
-[no]sr | Subreplicates | Yes/No | Yes
-random | Randomize input order of species | Yes/No | No
-multsets | Analyze multiple data sets | Yes/No | No
-printdata | Print out the data at start of run | Yes/No | No
-progress | Print indications of progress of run | Yes/No | No
Advanced qualifiers | Allowed values | Default
(none)

## Data files

## Notes

Multiple sequences sets not implemented yet!.

## References

## Warnings

## Diagnostics

## Exit status

## Known bugs

## See also

## Author(s)

(c) Copyright 1991-1993 by Joseph Felsenstein and 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 application was modified for inclusion in EMBOSS by Ian Longden (il@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

## Priority

## Target users

## Comments