edollop

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Function

Description

Phylip dollop documentation.

Usage

% edollop Dollo and polymorphism parsimony algorithm Phylip dollop program input file: dollop.dat Phylip dollop program output file [edollop.outfile]: Create a tree file [Y]: Phylip tree output file [edollop.treefile]:

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

Command line arguments

Dollo and polymorphism parsimony algorithm
Version: EMBOSS:6.5.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-datafile]          infile     Phylip dollop program input file
*  -datasets           integer    [2] Number of sets (Integer 2 or more)
*  -randseed           integer    [3] Random number seed (must be odd) (Any
                                  integer value)
*  -randtimes          integer    [3] How many times to randomise (Any integer
                                  value)
*  -valthresh          float      [1.0] Threshold value (Number 1.000 or more)
  [-outfile]           outfile    [edollop.outfile] Phylip dollop program
                                  output file
  [-[no]trout]         toggle     [Y] Create a tree file
*  -treefile           outfile    [edollop.treefile] Phylip tree output file

   Additional (Optional) qualifiers (* if not always prompted):
   -multsets           toggle     [N] Analyze multiple data sets
   -ancest             boolean    [N] Use ancestral states in input file
   -[no]besttree       toggle     [Y] Search for best tree
*  -random             toggle     [N] Randomize input order of species
   -[no]dollo          boolean    [Y] Do Dollo (else Polymorphism)
   -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
   -statesatnodes      boolean    [N] Print states at all nodes of tree
   -[no]drawtree       boolean    [Y] Draw tree

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

   Associated qualifiers:

   "-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
[-datafile] (Parameter 1)	infile	Phylip dollop program input file	Input file	Required
-datasets	integer	Number of sets	Integer 2 or more	2
-randseed	integer	Random number seed (must be odd)	Any integer value	3
-randtimes	integer	How many times to randomise	Any integer value	3
-valthresh	float	Threshold value	Number 1.000 or more	1.0
[-outfile] (Parameter 2)	outfile	Phylip dollop program output file	Output file	edollop.outfile
[-[no]trout] (Parameter 3)	toggle	Create a tree file	Toggle value Yes/No	Yes
-treefile	outfile	Phylip tree output file	Output file	edollop.treefile
Additional (Optional) qualifiers
-multsets	toggle	Analyze multiple data sets	Toggle value Yes/No	No
-ancest	boolean	Use ancestral states in input file	Boolean value Yes/No	No
-[no]besttree	toggle	Search for best tree	Toggle value Yes/No	Yes
-random	toggle	Randomize input order of species	Toggle value Yes/No	No
-[no]dollo	boolean	Do Dollo (else Polymorphism)	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
-steps	boolean	Print out steps in each site	Boolean value Yes/No	No
-statesatnodes	boolean	Print states 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
"-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: dollop.dat

     5    6
Alpha     110110
Beta      110000
Gamma     100110
Delta     001001
Epsilon   001110

Output file format

Output files for usage example

File: edollop.outfile

Dollo and polymorphism parsimony algorithm, version 3.57c.650

Dollo parsimony method


               


One most parsimonious tree found:




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


requires a total of      3.000

File: edollop.treefile

(Delta,(Epsilon,(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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