MIX
MIX estimates phylogenies by some parsimony methods for discrete character data with two states (0 and 1). Allows use of the Wagner parsimony method, the Camin-Sokal parsimony method, or arbitrary mixtures of these. Also reconstructs ancestral states and allows weighting of characters (does not infer branch lengths). 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/mix.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)
Mixed parsimony algorithm, version 3.6
5 species, 6 characters
Wagner parsimony method
Name Characters
---- ----------
Alpha 11011 0
Beta 11000 0
Gamma 10011 0
Delta 00100 1
Epsilon 00111 0
4 trees in all found
+--Epsilon
+-----4
! +--Gamma
+--2
! ! +--Delta
--1 +-----3
! +--Beta
!
+-----------Alpha
remember: this is an unrooted tree!
requires a total of 9.000
steps in each character:
0 1 2 3 4 5 6 7 8 9
*-----------------------------------------
0! 2 2 2 1 1 1
From To Any Steps? State at upper node
( . means same as in the node below it on tree)
1 1?011 0
1 2 no ..... .
2 4 maybe .0... .
4 Epsilon yes 0.1.. .
4 Gamma no ..... .
2 3 yes ...00 .
3 Delta yes 001.. 1
3 Beta maybe .1... .
1 Alpha maybe .1... .
+--------Gamma
!
+--2 +--Epsilon
! ! +--4
! +--3 +--Delta
--1 !
! +-----Beta
!
+-----------Alpha
remember: this is an unrooted tree!
requires a total of 9.000
steps in each character:
0 1 2 3 4 5 6 7 8 9
*-----------------------------------------
0! 1 2 1 2 2 1
From To Any Steps? State at upper node
( . means same as in the node below it on tree)
1 1?011 0
1 2 no ..... .
2 Gamma maybe .0... .
2 3 maybe ...?? .
3 4 yes 001.. .
4 Epsilon maybe ...11 . 4 Delta yes ...00 1
3 Beta maybe .1.00 .
1 Alpha maybe .1... .
+--------Epsilon +--4 ! ! +-----Gamma ! +--2 --1 ! +--Delta ! +--3 ! +--Beta ! +-----------Alpha
remember: this is an unrooted tree!
requires a total of 9.000
steps in each character:
0 1 2 3 4 5 6 7 8 9
*----------------------------------------- 0! 2 2 2 1 1 1
From To Any Steps? State at upper node
( . means same as in the node below it on tree)
1 1?011 0
1 4 maybe .0... .
4 Epsilon yes 0.1.. .
4 2 no ..... .
2 Gamma no ..... .
2 3 yes ...00 .
3 Delta yes 0.1.. 1
3 Beta yes .1... .
1 Alpha maybe .1... .
+--------Gamma
+--2
! ! +-----Epsilon
! +--4
--1 ! +--Delta
! +--3
! +--Beta
!
+-----------Alpha
remember: this is an unrooted tree!
requires a total of 9.000
steps in each character:
0 1 2 3 4 5 6 7 8 9
*-----------------------------------------
0! 2 2 2 1 1 1
From To Any Steps? State at upper node
( . means same as in the node below it on tree)
1 1?011 0
1 2 maybe .0... .
2 Gamma no ..... .
2 4 maybe ?.?.. .
4 Epsilon maybe 0.1.. .
4 3 yes ...00 .
3 Delta yes 0.1.. 1
3 Beta yes 110.. .
1 Alpha maybe .1... .