CONSENSE

CONSENSE reads a file of computer-readable trees and prints out (and may also write out onto a file) a consensus tree. At the moment it carries out a family of consensus tree methods called the Ml (M-sub-L) methods (Margush and McMorris, 1981). These include strict consensus and majority rule consensus. Basically the consensus tree consists of monophyletic groups that occur as often as possible in the data. If a group occurs in more than 50% of all the input trees it will definitely appear in the consensus tree. Part of Phylip.
INPUT = phylip tree files

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

TEST SET OF INPUT TREES

(A,(B,(H,(D,(J,(((G,E),(F,I)),C))))));

(A,(B,(D,((J,H),(((G,E),(F,I)),C)))));

(A,(B,(D,(H,(J,(((G,E),(F,I)),C))))));

(A,(B,(E,(G,((F,I),((J,(H,D)),C))))));

(A,(B,(E,(G,((F,I),(((J,H),D),C))))));

(A,(B,(E,((F,I),(G,((J,(H,D)),C))))));

(A,(B,(E,((F,I),(G,(((J,H),D),C))))));

(A,(B,(E,((G,(F,I)),((J,(H,D)),C)))));

(A,(B,(E,((G,(F,I)),(((J,H),D),C)))));

TEST SET OUTPUT

Consensus tree program, version 3.6

Species in order:

  1. A

  2. B

  3. H

  4. D

  5. J

  6. G

  7. E

  8. F

  9. I

  10. C

Sets included in the consensus tree

Set (species in order)     How many times out of    9.00

.......**.                   9.00

..********                   9.00

..****.***                   6.00

..***.....                   6.00

..***....*                   6.00

..*.*.....                   4.00

..***..***                   2.00

Sets NOT included in consensus tree:

Set (species in order)     How many times out of    9.00

.....**...                   3.00

.....*****                   3.00

..**......                   3.00

.....****.                   3.00

..****...*                   2.00

.....*.**.                   2.00

..*.******                   2.00

....******                   2.00

...*******                   1.00

Extended majority rule consensus tree

CONSENSUS TREE:

the numbers on the branches indicate the number

of times the partition of the species into the two sets

which are separated by that branch occurred

among the trees, out of   9.00 trees

                                     +--------------------C

                              +--6.0-|             +------H

                              |      |      +--4.0-|

                              |      +--6.0-|      +------J

                       +--2.0-|             |

                       |      |             +-------------D

                       |      |

                +--6.0-|      |                    +------F

                |      |      +----------------9.0-|

                |      |                           +------I

         +--9.0-|      |

         |      |      +----------------------------------G

  +------|      |

  |      |      +-----------------------------------------E

  |      |

  |      +------------------------------------------------B

  +-------------------------------------------------------A

  remember: this is an unrooted tree!