EMBOSS: ednacomp

ednacomp

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Function

Conversion of PHYLIP's dnacomp

Description

EDNACOMP -- Embossified DNA Compatibility Program

Phylip dnacomp documentation.

Usage

Here is a sample session with ednacomp using the data:-

    5   13
Alpha     AACGUGGCCAAAU
Beta      AAGGUCGCCAAAC
Gamma     CAUUUCGUCACAA
Delta     GGUAUUUCGGCCU
Epsilon   GGGAUCUCGGCCC


% ednacomp test

DNA compatibility algorithm
Output file [ednacomp.outfile]: stdout
Create a tree file [Y]: 
Treefile name [ednacomp.treefile]: 
Outgroup root [N]: 


One most parsimonious tree found:




           +--Epsilon   
        +--4  
     +--3  +--Delta     
     !  !  
  +--2  +-----Gamma     
  !  !  
--1  +--------Beta      
  !  
  +-----------Alpha     

  remember: this is an unrooted tree!


total number of compatible sites is       11.0




% more ednacomp.treefile 
((((Epsilon,Delta),Gamma),Beta),Alpha);

Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-msf]               seqset     File containing a sequence allignment
  [-outfile]           outfile    Output file name
  [-[no]trout]         bool       Create a tree file
*  -treefile           outfile    Tree file name
   -og                 bool       Outgroup root
*  -outgnum            integer    number of the outgroup
*  -randseed           integer    Random number seed (must be odd)
*  -randtimes          integer    Number of times to jumble

   Optional qualifiers:
   -[no]drawtree       bool       Draw tree
   -printdata          bool       Print out the data at start of run
   -progress           bool       Print indications of progress of run
   -stepoutput         bool       Print steps & compatibility at sites
   -allnodes           bool       Print sequences at all nodes of tree
   -random             bool       Randomize input order of species

   Advanced qualifiers: (none)

Mandatory qualifiers Allowed values Default

[-msf]
(Parameter 1) File containing a sequence allignment Readable sequences Required

[-outfile]
(Parameter 2) Output file name Output file ednacomp.outfile

[-[no]trout]
(Parameter 3) Create a tree file Yes/No Yes

-treefile Tree file name Output file ednacomp.treefile

-og Outgroup root Yes/No No

-outgnum number of the outgroup Integer 1 or more 1

-randseed Random number seed (must be odd) Any integer value 0

-randtimes Number of times to jumble Any integer value 0

Optional qualifiers Allowed values Default

-[no]drawtree Draw tree Yes/No Yes

-printdata Print out the data at start of run Yes/No No

-progress Print indications of progress of run Yes/No No

-stepoutput Print steps & compatibility at sites Yes/No No

-allnodes Print sequences at all nodes of tree Yes/No No

-random Randomize input order of species Yes/No No

Advanced qualifiers Allowed values Default

(none)

Mandatory qualifiers	Allowed values	Default
[-msf] (Parameter 1)	File containing a sequence allignment	Readable sequences	Required
[-outfile] (Parameter 2)	Output file name	Output file	ednacomp.outfile
[-[no]trout] (Parameter 3)	Create a tree file	Yes/No	Yes
-treefile	Tree file name	Output file	ednacomp.treefile
-og	Outgroup root	Yes/No	No
-outgnum	number of the outgroup	Integer 1 or more	1
-randseed	Random number seed (must be odd)	Any integer value	0
-randtimes	Number of times to jumble	Any integer value	0
Optional qualifiers	Allowed values	Default
-[no]drawtree	Draw tree	Yes/No	Yes
-printdata	Print out the data at start of run	Yes/No	No
-progress	Print indications of progress of run	Yes/No	No
-stepoutput	Print steps & compatibility at sites	Yes/No	No
-allnodes	Print sequences at all nodes of tree	Yes/No	No
-random	Randomize input order of species	Yes/No	No
Advanced qualifiers	Allowed values	Default
(none)

Input file format

Output file format

Data files

Notes

References

Warnings

Diagnostics

Exit status

Known bugs

Author(s)

(c) Copyright 1986-1993 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.