edolpenny

Wiki

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

Function

Conversion of PHYLIP's dolpenny

Description

EDOLPENNY - Branch and bound to find all most parsimonious trees for Dollo, polymorphism parsimony criteria

Usage

Here is a sample session with edolpenny using the data:-
```    7    6
Alpha1    110110
Alpha2    110110
Beta1     110000
Beta2     110000
Gamma1    100110
Delta     001001
Epsilon   001110

```
```
% edolpenny test

Penny algorithm Dollo or polymorphism
Output file [edolpenny.outfile]: stdout
Dollo Parsimony method (else Polymorphis) [Y]:
Create a tree file [Y]:
Output treefile name [edolpenny.treefile]:

Penny algorithm for Dollo or polymorphism parsimony, version 3.573c
branch-and-bound to find all most parsimonious trees

Dollo parsimony method

requires a total of              3.000

3 trees in all found

+-----------------Delta
!
--2  +--------------Epsilon
!  !
+--3  +-----------Gamma1
!  !
+--6  +--------Alpha2
!  !
+--1     +--Beta2
!  +--5
+--4  +--Beta1
!
+-----Alpha1

+-----------------Delta
!
--2  +--------------Epsilon
!  !
+--3  +-----------Gamma1
!  !
+--6        +--Beta2
!  +-----5
!  !     +--Beta1
+--4
!     +--Alpha2
+-----1
+--Alpha1

+-----------------Delta
!
--2  +--------------Epsilon
!  !
+--3  +-----------Gamma1
!  !
!  !        +--Beta2
+--6     +--5
!  +--4  +--Beta1
!  !  !
+--1  +-----Alpha2
!
+--------Alpha1

% more edolpenny.treefile
(Delta,(Epsilon,(Gamma1,(Alpha2,((Beta2,Beta1),Alpha1)))))[0.3333];
(Delta,(Epsilon,(Gamma1,((Beta2,Beta1),(Alpha2,Alpha1)))))[0.3333];
(Delta,(Epsilon,(Gamma1,(((Beta2,Beta1),Alpha2),Alpha1))))[0.3333];

```

Command line arguments

 ``` Mandatory qualifiers (* if not always prompted): [-datafile] infile data file [-outfile] outfile Output file name [-[no]dollo] bool Dollo Parsimony method (else Polymorphis) * -valthresh float threshold value * -datasets integer number of sets [-[no]trout] bool Create a tree file * -treefile outfile Tree file name Optional qualifiers: -numgroups integer How many groups of 100 trees -howoften integer How often to report, in trees -simple bool Branch and bound is simple -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 Input file Required
[-outfile]
(Parameter 2)
Output file name Output file edolpenny.outfile
[-[no]dollo]
(Parameter 3)
Dollo Parsimony method (else Polymorphis) Yes/No Yes
-valthresh threshold value Number 1.000 or more 1.0
-datasets number of sets Integer 2 or more 2
[-[no]trout]
(Parameter 4)
Create a tree file Yes/No Yes
-treefile Tree file name Output file edolpenny.treefile
Optional qualifiers Allowed values Default
-numgroups How many groups of 100 trees Any integer value 1000
-howoften How often to report, in trees Any integer value 100
-simple Branch and bound is simple Yes/No No
-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
-thresh Use Threshold parsimony Yes/No No

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.

```