EMBOSS: eneighbor

eneighbor

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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)

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

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.