EMBOSS: edollop

edollop

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Function

Conversion of PHYLIP's dollop

Description

EDOLLOP -- Embossified Dollo and Polymorphism Parsimony Program

Phylip dollop documentation.

Usage

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

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


% edollop test

Dollo and polymorphism parsimony algorithm
Output file [edollop.outfile]: stdout
Create a tree file [Y]: 
Output treefile name [edollop.treefile]: 

Dollo and polymorphism parsimony algorithm, version 3.573c

Dollo parsimony method


               


One most parsimonious tree found:




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


requires a total of      3.000




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

Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-datafile]          infile     data file to be read in
  [-outfile]           outfile    Output file name
*  -randseed           integer    Random number seed (must be odd)
*  -randtimes          integer    How many times to randomise
*  -valthresh          float      threshold value
*  -datasets           integer    number of sets
  [-[no]trout]         bool       Create a tree file
*  -treefile           outfile    Tree file name

   Optional qualifiers (* if not always prompted):
   -[no]besttree       bool       Search for best tree
*  -random             bool       Randomize input order of species
   -[no]dollo          bool       Do Dollo (else Polymorphism)
   -ancest             bool       Use ancestral states in input file
   -multsets           bool       Analyze multiple data sets
   -printdata          bool       Print out the data at start of run
   -progress           bool       Print indications of progress of run
   -steps              bool       Print out steps in each site
   -statesatnodes      bool       Print states at all nodes of tree
   -[no]drawtree       bool       Draw tree

   Advanced qualifiers:
   -thresh             bool       Use Threshold parsimony

Mandatory qualifiers Allowed values Default

[-datafile]
(Parameter 1) data file to be read in Input file Required

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

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

-randtimes How many times to randomise Any integer value 3

-valthresh threshold value Number 1.000 or more 1.0

-datasets number of sets Integer 2 or more 2

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

-treefile Tree file name Output file edollop.treefile

Optional qualifiers Allowed values Default

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

-random Randomize input order of species Yes/No No

-[no]dollo Do Dollo (else Polymorphism) Yes/No Yes

-ancest Use ancestral states in input file Yes/No No

-multsets Analyze multiple data sets Yes/No No

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

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

-steps Print out steps in each site Yes/No No

-statesatnodes Print states at all nodes of tree Yes/No No

-[no]drawtree Draw tree Yes/No Yes

Advanced qualifiers Allowed values Default

-thresh Use Threshold parsimony Yes/No No

Mandatory qualifiers	Allowed values	Default
[-datafile] (Parameter 1)	data file to be read in	Input file	Required
[-outfile] (Parameter 2)	Output file name	Output file	edollop.outfile
-randseed	Random number seed (must be odd)	Any integer value	3
-randtimes	How many times to randomise	Any integer value	3
-valthresh	threshold value	Number 1.000 or more	1.0
-datasets	number of sets	Integer 2 or more	2
[-[no]trout] (Parameter 3)	Create a tree file	Yes/No	Yes
-treefile	Tree file name	Output file	edollop.treefile
Optional qualifiers	Allowed values	Default
-[no]besttree	Search for best tree	Yes/No	Yes
-random	Randomize input order of species	Yes/No	No
-[no]dollo	Do Dollo (else Polymorphism)	Yes/No	Yes
-ancest	Use ancestral states in input file	Yes/No	No
-multsets	Analyze multiple data sets	Yes/No	No
-printdata	Print out the data at start of run	Yes/No	No
-progress	Print indications of progress of run	Yes/No	No
-steps	Print out steps in each site	Yes/No	No
-statesatnodes	Print states at all nodes of tree	Yes/No	No
-[no]drawtree	Draw tree	Yes/No	Yes
Advanced qualifiers	Allowed values	Default
-thresh	Use Threshold parsimony	Yes/No	No

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.