ednacomp

 

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Function

DNA compatibility algorithm

Description

EDNACOMP -- Embossified DNA Compatibility Program

Phylip dnacomp documentation.

Usage

Here is a sample session with ednacomp 


% ednacomp -stepoutput 
DNA compatibility algorithm
Input (aligned) nucleotide sequence set: dnacomp.dat
Outgroup root [N]: 
Randomize input order of species [N]: 
Phylip dnacomp program output file [ednacomp.outfile]: 
Create a tree file [Y]: 
Phylip tree output file [ednacomp.treefile]:

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

Command line arguments 

DNA compatibility algorithm
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-sequence]          seqset     File containing a sequence alignment
   -og                 toggle     [N] Outgroup root
*  -outgnum            integer    [1] Number of the outgroup (Integer 1 or
                                  more)
   -random             toggle     [N] Randomize input order of species
*  -randseed           integer    [0] Random number seed (must be odd) (Any
                                  integer value)
*  -randtimes          integer    [0] Number of times to jumble (Any integer
                                  value)
  [-outfile]           outfile    [ednacomp.outfile] Phylip dnacomp program
                                  output file
  [-[no]trout]         toggle     [Y] Create a tree file
*  -treefile           outfile    [ednacomp.treefile] Phylip tree output file

   Additional (Optional) qualifiers:
   -[no]drawtree       boolean    [Y] Draw tree
   -printdata          boolean    [N] Print out the data at start of run
   -progress           boolean    [N] Print indications of progress of run
   -stepoutput         boolean    [N] Print steps & compatibility at sites
   -allnodes           boolean    [N] Print sequences at all nodes of tree

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

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   "-treefile" 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

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-sequence]
(Parameter 1)		 seqset File containing a sequence alignment Readable set of sequences Required
-og toggle Outgroup root Toggle value Yes/No No
-outgnum integer Number of the outgroup Integer 1 or more 1
-random toggle Randomize input order of species Toggle value Yes/No No
-randseed integer Random number seed (must be odd) Any integer value 0
-randtimes integer Number of times to jumble Any integer value 0
[-outfile]
(Parameter 2)		 outfile Phylip dnacomp program output file Output file ednacomp.outfile
[-[no]trout]
(Parameter 3)		 toggle Create a tree file Toggle value Yes/No Yes
-treefile outfile Phylip tree output file Output file ednacomp.treefile
Additional (Optional) qualifiers
-[no]drawtree boolean Draw tree Boolean value Yes/No Yes
-printdata boolean Print out the data at start of run Boolean value Yes/No No
-progress boolean Print indications of progress of run Boolean value Yes/No No
-stepoutput boolean Print steps & compatibility at sites Boolean value Yes/No No
-allnodes boolean Print sequences at all nodes of tree Boolean value Yes/No No
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-sequence" associated seqset qualifiers
-sbegin1
-sbegin_sequence		 integer Start of each sequence to be used Any integer value 0
-send1
-send_sequence		 integer End of each sequence to be used Any integer value 0
-sreverse1
-sreverse_sequence		 boolean Reverse (if DNA) Boolean value Yes/No N
-sask1
-sask_sequence		 boolean Ask for begin/end/reverse Boolean value Yes/No N
-snucleotide1
-snucleotide_sequence		 boolean Sequence is nucleotide Boolean value Yes/No N
-sprotein1
-sprotein_sequence		 boolean Sequence is protein Boolean value Yes/No N
-slower1
-slower_sequence		 boolean Make lower case Boolean value Yes/No N
-supper1
-supper_sequence		 boolean Make upper case Boolean value Yes/No N
-scircular1
-scircular_sequence		 boolean Sequence is circular Boolean value Yes/No N
-squick1
-squick_sequence		 boolean Read id and sequence only Boolean value Yes/No N
-sformat1
-sformat_sequence		 string Input sequence format Any string  
-iquery1
-iquery_sequence		 string Input query fields or ID list Any string  
-ioffset1
-ioffset_sequence		 integer Input start position offset Any integer value 0
-sdbname1
-sdbname_sequence		 string Database name Any string  
-sid1
-sid_sequence		 string Entryname Any string  
-ufo1
-ufo_sequence		 string UFO features Any string  
-fformat1
-fformat_sequence		 string Features format Any string  
-fopenfile1
-fopenfile_sequence		 string Features file name Any string  
"-outfile" associated outfile qualifiers
-odirectory2
-odirectory_outfile		 string Output directory Any string  
"-treefile" associated outfile qualifiers
-odirectory string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

Input file format

Input files for usage example

File: dnacomp.dat

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

Output file format

Output files for usage example

File: ednacomp.outfile



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


 steps in each site:
         0   1   2   3   4   5   6   7   8   9
     *-----------------------------------------
    0!       2   1   3   2   0   2   1   1   1
   10!   1   1   1   3                        

 compatibility (Y or N) of each site with this tree:

      0123456789
     *----------
   0 ! YYNYYYYYY
  10 !YYYN

File: ednacomp.treefile

((((Epsilon,Delta),Gamma),Beta),Alpha);

Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostics

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program name Description
distmat Create a distance matrix from a multiple sequence alignment
ednadist Nucleic acid sequence distance matrix program
ednainvar Nucleic acid sequence invariants method
ednaml Phylogenies from nucleic acid maximum likelihood
ednamlk Phylogenies from nucleic acid maximum likelihood with clock
ednapars DNA parsimony algorithm
ednapenny Penny algorithm for DNA
eprotdist Protein distance algorithm
eprotpars Protein parsimony algorithm
erestml Restriction site maximum likelihood method
eseqboot Bootstrapped sequences algorithm
fdiscboot Bootstrapped discrete sites algorithm
fdnacomp DNA compatibility algorithm
fdnadist Nucleic acid sequence distance matrix program
fdnainvar Nucleic acid sequence invariants method
fdnaml Estimate nucleotide phylogeny by maximum likelihood
fdnamlk Estimates nucleotide phylogeny by maximum likelihood
fdnamove Interactive DNA parsimony
fdnapars DNA parsimony algorithm
fdnapenny Penny algorithm for DNA
fdolmove Interactive Dollo or polymorphism parsimony
ffreqboot Bootstrapped genetic frequencies algorithm
fproml Protein phylogeny by maximum likelihood
fpromlk Protein phylogeny by maximum likelihood
fprotdist Protein distance algorithm
fprotpars Protein parsimony algorithm
frestboot Bootstrapped restriction sites algorithm
frestdist Calculate distance matrix from restriction sites or fragments
frestml Restriction site maximum likelihood method
fseqboot Bootstrapped sequences algorithm
fseqbootall Bootstrapped sequences algorithm

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.

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments 

None