DOLLOP

DOLLOP. This program carries out the Dollo and polymorphism parsimony methods. The Dollo parsimony method was first suggested in print in verbal form by Le Quesne (1974) and was first well-specified by Farris (1977). The method is named after Louis Dollo since he was one of the first to assert that in evolution it is harder to gain a complex feature than to lose it. The algorithm explains the presence of the state 1 by allowing up to one forward change 0-->1 and as many reversions 1-->0 as are necessary to explain the pattern of states seen. The program attempts to minimize the number of 1-->0 reversions necessary. Part of Phylip.

© Copyright 1991-2006 by the University of Washington. Written by Joseph Felsenstein. Edited by NGBW team.

Manual: http://evolution.genetics.washington.edu/phylip/doc/dollop.html

INPUT: Discrete Character Matrix

TEST DATA SET

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

TEST SET OUTPUT (with all numerical options on)

Dollo and polymorphism parsimony algorithm, version 3.6
Dollo parsimony method

 5 species, 6 characters

Name    Characters
----    ----------
Alpha    11011 0
Beta     11000 0
Gamma    10011 0
Delta    00100 1
Epsilon  00111 0
One most parsimonious tree found: 
  +-----------Delta 
--3
  !  +--------Epsilon
  +--4
     !  +-----Gamma
     +--2
        !  +--Beta
        +--1
           +--Alpha

requires a total of 3.000
reversions in each character:

      0 1 2 3 4 5 6 7 8 9
  *-----------------------------------------
 0!     0 0 1 1 1 0 
From To Any Steps? State at upper node
 ( . means same as in the node below it on tree)

root    3     yes ..1.. .
 3    Delta   yes ..... 1
 3      4     yes ...11 .
 4   Epsilon   no ..... .
 4      2     yes 1.0.. .
 2    Gamma    no ..... .
 2      1     yes .1... .
 1     Beta   yes ...00 .
 1    Alpha    no ..... .