EMBOSS: ednapars

ednapars

Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

Function

DNA parsimony algorithm

Description

EDNAPARS -- Embossified DNA Parsimony Program

Phylip dnapars documentation.

Usage

Here is a sample session with ednapars

% ednapars DNA parsimony algorithm Input (aligned) nucleotide sequence set: dnapars.dat Randomize input order of species [N]: Phylip dnapars program output file [ednapars.outfile]: Create a tree file [Y]: Phylip tree output file [ednapars.treefile]:

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

Command line arguments

DNA parsimony algorithm
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-sequence]          seqset     File containing a sequence allignment
*  -random             toggle     [N] Randomize input order of species
*  -randseed           integer    [3] Random number seed (must be odd) (Any
                                  integer value)
*  -randtimes          integer    [3] How many times to randomise (Any integer
                                  value)
*  -outgnum            integer    [1] Number of the outgroup (Integer 1 or
                                  more)
*  -valthresh          float      [1.0] Threshold value (Number 1.000 or more)
  [-outfile]           outfile    [ednapars.outfile] Phylip dnapars program
                                  output file
  [-[no]trout]         toggle     [Y] Create a tree file
*  -treefile           outfile    [ednapars.treefile] Phylip tree output file

   Additional (Optional) qualifiers:
   -[no]besttree       toggle     [Y] Search for best tree
   -og                 toggle     [N] Outgroup root
   -printdata          boolean    [N] Print out the data at start of run
   -progress           boolean    [N] Print indications of progress of run
   -steps              boolean    [N] Print out steps in each site
   -seqatnodes         boolean    [N] Print sequences at all nodes of tree
   -[no]drawtree       boolean    [Y] Draw tree

   Advanced (Unprompted) qualifiers:
   -thresh             toggle     [N] Use Threshold parsimony

   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 allignment Readable set of sequences Required

-random toggle Randomize input order of species Toggle value Yes/No No

-randseed integer Random number seed (must be odd) Any integer value 3

-randtimes integer How many times to randomise Any integer value 3

-outgnum integer Number of the outgroup Integer 1 or more 1

-valthresh float Threshold value Number 1.000 or more 1.0

[-outfile]
(Parameter 2) outfile Phylip dnapars program output file Output file ednapars.outfile

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

-treefile outfile Phylip tree output file Output file ednapars.treefile

Additional (Optional) qualifiers

-[no]besttree toggle Search for best tree Toggle value Yes/No Yes

-og toggle Outgroup root Toggle value Yes/No No

-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

-steps boolean Print out steps in each site Boolean value Yes/No No

-seqatnodes boolean Print sequences at all nodes of tree Boolean value Yes/No No

-[no]drawtree boolean Draw tree Boolean value Yes/No Yes

Advanced (Unprompted) qualifiers

-thresh toggle Use Threshold parsimony Toggle value Yes/No No

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

Qualifier	Type	Description	Allowed values	Default
Standard (Mandatory) qualifiers
[-sequence] (Parameter 1)	seqset	File containing a sequence allignment	Readable set of sequences	Required
-random	toggle	Randomize input order of species	Toggle value Yes/No	No
-randseed	integer	Random number seed (must be odd)	Any integer value	3
-randtimes	integer	How many times to randomise	Any integer value	3
-outgnum	integer	Number of the outgroup	Integer 1 or more	1
-valthresh	float	Threshold value	Number 1.000 or more	1.0
[-outfile] (Parameter 2)	outfile	Phylip dnapars program output file	Output file	ednapars.outfile
[-[no]trout] (Parameter 3)	toggle	Create a tree file	Toggle value Yes/No	Yes
-treefile	outfile	Phylip tree output file	Output file	ednapars.treefile
Additional (Optional) qualifiers
-[no]besttree	toggle	Search for best tree	Toggle value Yes/No	Yes
-og	toggle	Outgroup root	Toggle value Yes/No	No
-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
-steps	boolean	Print out steps in each site	Boolean value Yes/No	No
-seqatnodes	boolean	Print sequences at all nodes of tree	Boolean value Yes/No	No
-[no]drawtree	boolean	Draw tree	Boolean value Yes/No	Yes
Advanced (Unprompted) qualifiers
-thresh	toggle	Use Threshold parsimony	Toggle value Yes/No	No
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: dnapars.dat

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

Output file format

Output files for usage example

File: ednapars.outfile


One most parsimonious tree found:




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

  remember: this is an unrooted tree!


requires a total of     19.000

File: ednapars.treefile

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

Data files

None.

Notes

Multiple sequences sets not implemented yet!.

References

None.

Warnings

None.

Diagnostics

None.

Exit status

It always exits with status 0.

Known bugs

None.

Program name	Description
distmat	Create a distance matrix from a multiple sequence alignment
ednacomp	DNA compatibility algorithm
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
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

Wiki

Function

Description

Usage

Command line arguments

Input file format

Input files for usage example

File: dnapars.dat

Output file format

Output files for usage example

File: ednapars.outfile

File: ednapars.treefile

Data files

Notes

References

Warnings

Diagnostics

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments