ednapars

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Function

Description

Phylip dnapars documentation.

Usage

% 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:6.5.0.0

   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
   -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
-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

Notes

References

Warnings

Diagnostics

Exit status

Known bugs

See also

Author(s)

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

Comments

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