GRIMM - Genome rearrangement algorithms

# genomes:      
Genome 1:
Genome 2:
Genome 3:
Chromosomes:
Signs:
           Or,

Multiple genome options

Action:
Tree size: Edge length proportional to distance       Total width of tree
Not proportional      

Pairwise scenario formatting options

Report Style:
One line per genome
(chromosomes concatenated)
  One column
(chromosomes separated)
  Two column before & after
(chromosomes separated)
Horizontal
Vertical
  Yes   Show all chromosomes
Only affected chromosomes
Show all possible initial steps of optimal scenarios
Highlighting style: Should operations (reversal, translocation, fission, fusion) be highlighted, and when?
Chromosome end
format:
Color coding: Genes should be colored according to their chromosome in which genome:
Click here or scroll up to enter new data or change options.

MGR Report

First studied by Cosner et al, 2000 using GRAPPA. It consists of 13 cpDNAs with 105 markers. Click here for details.

Tree recovered (Newick Standard)

(Platycodon:11,(Codonopsis:5,Cyananthus:5)A22:3,(((Asyneuma:5,(Legousia:4,Triodanus:1)A19:2)A20:4,((Merciera:4,Wahlenbergia:2)A16:4,((Adenophora:3,Campanula:0)A14:1,(Symphyandra:1,Trachelium:0)A13:0)A15:0)A17:1)A18:7,Tobacco:2)A21:0)A23;

Score: 65 rearrangements

All ancestral nodes are coded by the letter A followed by a number (e.g. A9). Click here or scroll down to view the gene order sequence of the genomes used as input and of the ancestors recovered.

ASCII representation of the unrooted tree recovered

  +----------------11-------------------Platycodon
  |  
  |             +-------5--------Codonopsis
  |  +---3----A22  
  |  |          +-------5--------Cyananthus
  |  |  
  |  |                                         +-------5--------Asyneuma
  |  |                           +-----4-----A20  
  |  |                           |             |       +-----4------Legousia
  |  |                           |             +--2--A19  
  +A23                           |                     +1-Triodanus
     |  +----------7-----------A18  
     |  |                        |                 +-----4------Merciera
     |  |                        |   +-----4-----A16  
     |  |                        |   |             +-2---Wahlenbergia
     |  |                        |   |  
     |  |                        +1A17     +---3-----Adenophora
     +A21                            |  +1A14 
        |                            |  |  +-Campanula
        |                            +A15  
        |                               |  +1-Symphyandra
        |                               +A13  
        |                                  +-Trachelium
        |  
        +-2---Tobacco

The number of rearrangements that occured on each edge is shown. When no number is shown on an edge it means that no rearrangement occured on that edge. To view actual rearrangements events, click on an edge; it will describe one of the possible optimal sequence of rearrangements. It is also possible to click on the name of a node to view its gene sequence below.



Pairwise distance matrix of the input genomes (leaf nodes)


  Trachelium Campanula Adenophora Symphyandra Legousia Asyneuma Triodanus Wahlenbergia Merciera Codonopsis Cyananthus Platycodon Tobacco
Trachelium 0 1 4 1 8 10 8 5 8 15 14 19 10
Campanula 1 0 3 2 9 11 9 6 9 15 15 20 11
Adenophora 4 3 0 5 12 14 12 8 11 16 15 20 13
Symphyandra 1 2 5 0 9 11 9 6 9 14 13 20 11
Legousia 8 9 12 9 0 9 5 12 14 18 16 23 14
Asyneuma 10 11 14 11 9 0 5 12 16 18 16 21 12
Triodanus 8 9 12 9 5 5 0 12 14 18 15 21 12
Wahlenbergia 5 6 8 6 12 12 12 0 6 18 16 23 14
Merciera 8 9 11 9 14 16 14 6 0 17 16 24 16
Codonopsis 15 15 16 14 18 18 18 18 17 0 8 18 10
Cyananthus 14 15 15 13 16 16 15 16 16 8 0 16 10
Platycodon 19 20 20 20 23 21 21 23 24 18 16 0 13
Tobacco 10 11 13 11 14 12 12 14 16 10 10 13 0

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Gene order sequence of the genomes used as input and of the ancestors recovered

Trachelium
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -60 -59 -58 -57 -56 -53 -52 -51 -50 -49 37 38 39 40 -35 -34 -33 -32 -31 -30 -29 -28 -27 -26 -44 -43 -42 -41 45 46 47 48 -36 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -90 -89 -88 -87 -86 -85 -84 77 78 79 80 81 82 83 91 92 93 94 95 96 -55 -54 -105 -104 -103 -102 -101 -100 -99 -98 -97

Campanula
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -60 -59 -58 -57 -56 -53 -52 -51 -50 -49 -39 -38 -37 40 -35 -34 -33 -32 -31 -30 -29 -28 -27 -26 -44 -43 -42 -41 45 46 47 48 -36 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -90 -89 -88 -87 -86 -85 -84 77 78 79 80 81 82 83 91 92 93 94 95 96 -55 -54 -105 -104 -103 -102 -101 -100 -99 -98 -97

Adenophora
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -60 -59 -58 -57 -56 -53 -52 -51 -50 -49 -39 -38 -37 28 29 30 31 32 33 34 35 40 26 27 -44 -43 -42 -41 45 46 47 48 -36 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -90 -89 -88 -87 -86 -85 -84 77 78 79 80 81 82 83 91 92 93 94 95 96 -55 -54 -105 -104 -103 -102 -101 -100 -99 -98 -97

Symphyandra
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -60 -59 -58 -57 -56 -39 -38 -37 49 50 51 52 53 40 -35 -34 -33 -32 -31 -30 -29 -28 -27 -26 -44 -43 -42 -41 45 46 47 48 -36 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -90 -89 -88 -87 -86 -85 -84 77 78 79 80 81 82 83 91 92 93 94 95 96 -55 -54 -105 -104 -103 -102 -101 -100 -99 -98 -97

Legousia
1 2 3 4 9 10 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -60 -59 -58 -57 -56 -27 -26 -44 -43 -42 -41 45 46 47 48 -36 -35 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -90 -89 -88 -87 -86 -85 -84 77 78 79 80 81 82 83 91 92 93 94 95 96 5 6 7 8 -55 -54 -53 -105 -104 -103 -102 -101 -100 -99 -98 28 29 30 31 32 33 34 -40 -39 -38 -37 49 50 51 52 -97

Asyneuma
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -56 -55 -54 -53 -60 -59 -58 -57 -27 -26 -44 -43 -42 -41 45 46 47 48 -36 -35 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -89 -88 -87 -86 -85 -84 77 78 79 80 81 82 83 90 91 92 93 94 95 96 -105 -104 -103 -102 -101 -100 -99 -98 28 29 30 31 32 33 34 -40 -39 -38 -37 49 50 51 52 -97

Triodanus
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -60 -59 -58 -57 -56 -27 -26 -44 -43 -42 -41 45 46 47 48 -36 -35 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -89 -88 -87 -86 -85 -84 77 78 79 80 81 82 83 90 91 92 93 94 95 96 -55 -54 -53 -105 -104 -103 -102 -101 -100 -99 -98 28 29 30 31 32 33 34 -40 -39 -38 -37 49 50 51 52 -97

Wahlenbergia
1 2 3 4 5 6 7 8 9 10 11 -60 -59 -58 -57 -56 -53 -52 -51 -50 -49 37 38 39 40 -35 -34 -33 -32 -31 -30 -29 -28 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -27 -26 -44 -43 -42 -41 45 46 47 48 -36 54 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -90 -89 -88 -87 -86 -85 -84 77 78 79 80 81 82 83 91 92 93 94 95 96 -55 -105 -104 -103 -102 -101 -100 -99 -98 -97

Merciera
1 2 3 4 5 6 7 8 9 10 49 50 51 52 53 28 29 30 31 32 33 34 35 -40 -39 -38 -37 -60 -59 -58 -57 -56 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -27 -26 -44 -43 -42 -41 45 46 47 48 -36 54 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -90 -89 -88 -87 -86 -85 77 78 79 80 81 82 83 84 91 92 93 94 95 96 -55 -105 -104 -103 -102 -101 -100 -99 -98 -97

Codonopsis
1 2 3 4 5 6 7 8 -36 -35 -34 -33 -32 -31 -30 -29 -28 -27 -26 -25 -24 -23 -22 -21 -20 -19 -18 -15 -14 -13 -12 -11 -10 -9 40 56 57 58 59 60 37 38 39 -44 -43 -42 -41 45 46 47 48 49 50 51 52 53 16 17 54 55 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 -96 -95 -94 -93 -92 -91 -90 -89 -88 -87 -86 -85 -84 -83 -82 -81 -80 -79 -78 -77 -105 -104 -103 -102 -101 -100 -99 -98 -97

Cyananthus
1 2 3 4 5 6 7 8 28 -36 -35 -34 -33 -32 -31 -30 -29 -27 -26 40 56 57 58 59 60 37 38 39 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -15 -14 -13 -12 -11 -10 -9 -44 -43 -42 -41 45 46 47 48 -55 -54 -53 -52 -51 -50 -49 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 -105 -104 -103 -102 -101 -100 -99 -98 -97

Platycodon
1 8 2 3 4 5 29 30 31 32 33 34 35 36 -56 -55 -54 -53 -52 -51 -50 -28 -27 -26 9 -49 -48 -47 -46 -45 41 42 43 44 37 38 39 40 16 17 18 19 20 21 22 23 24 25 10 11 12 13 14 15 57 58 59 6 7 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 -105 -104 -103 -102 -101 -100 -99 -98 -97

Tobacco
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105

A13
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -60 -59 -58 -57 -56 -53 -52 -51 -50 -49 37 38 39 40 -35 -34 -33 -32 -31 -30 -29 -28 -27 -26 -44 -43 -42 -41 45 46 47 48 -36 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -90 -89 -88 -87 -86 -85 -84 77 78 79 80 81 82 83 91 92 93 94 95 96 -55 -54 -105 -104 -103 -102 -101 -100 -99 -98 -97

A14
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -60 -59 -58 -57 -56 -53 -52 -51 -50 -49 -39 -38 -37 40 -35 -34 -33 -32 -31 -30 -29 -28 -27 -26 -44 -43 -42 -41 45 46 47 48 -36 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -90 -89 -88 -87 -86 -85 -84 77 78 79 80 81 82 83 91 92 93 94 95 96 -55 -54 -105 -104 -103 -102 -101 -100 -99 -98 -97

A15
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -60 -59 -58 -57 -56 -53 -52 -51 -50 -49 37 38 39 40 -35 -34 -33 -32 -31 -30 -29 -28 -27 -26 -44 -43 -42 -41 45 46 47 48 -36 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -90 -89 -88 -87 -86 -85 -84 77 78 79 80 81 82 83 91 92 93 94 95 96 -55 -54 -105 -104 -103 -102 -101 -100 -99 -98 -97

A16
1 2 3 4 5 6 7 8 9 10 49 50 51 52 53 56 57 58 59 60 28 29 30 31 32 33 34 35 -40 -39 -38 -37 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -27 -26 -44 -43 -42 -41 45 46 47 48 -36 54 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -90 -89 -88 -87 -86 -85 -84 77 78 79 80 81 82 83 91 92 93 94 95 96 -55 -105 -104 -103 -102 -101 -100 -99 -98 -97

A17
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -60 -59 -58 -57 -56 -53 -52 -51 -50 -49 37 38 39 40 -35 -34 -33 -32 -31 -30 -29 -28 -27 -26 -44 -43 -42 -41 45 46 47 48 -36 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -90 -89 -88 -87 -86 -85 -84 77 78 79 80 81 82 83 91 92 93 94 95 96 -55 -54 -105 -104 -103 -102 -101 -100 -99 -98 -97

A18
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -60 -59 -58 -57 -56 -53 -52 -51 -50 -49 37 38 39 40 -35 -34 -33 -32 -31 -30 -29 -28 -27 -26 -44 -43 -42 -41 45 46 47 48 -36 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -83 -82 -81 -80 -79 -78 -77 84 85 86 87 88 89 90 91 92 93 94 95 96 -55 -54 -105 -104 -103 -102 -101 -100 -99 -98 -97

A19
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -60 -59 -58 -57 -56 -27 -26 -44 -43 -42 -41 45 46 47 48 -36 -35 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -83 -82 -81 -80 -79 -78 -77 84 85 86 87 88 89 90 91 92 93 94 95 96 -55 -54 -53 -105 -104 -103 -102 -101 -100 -99 -98 28 29 30 31 32 33 34 -40 -39 -38 -37 49 50 51 52 -97

A20
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -60 -59 -58 -57 -56 -105 -104 -103 -102 -101 -100 -99 -98 28 29 30 31 32 33 34 -40 -39 -38 -37 49 50 51 52 53 54 55 -96 -95 -94 -93 -92 -91 -90 -89 -88 -87 -86 -85 -84 77 78 79 80 81 82 83 16 17 18 19 20 21 22 23 24 25 35 36 -48 -47 -46 -45 41 42 43 44 26 27 -97

A21
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 -44 -43 -42 -41 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 -105 -104 -103 -102 -101 -100 -99 -98 -97

A22
1 2 3 4 5 6 7 8 -40 -39 -38 -37 -60 -59 -58 -57 -56 -36 -35 -34 -33 -32 -31 -30 -29 -28 -27 -26 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -15 -14 -13 -12 -11 -10 -9 -44 -43 -42 -41 45 46 47 48 49 50 51 52 53 54 55 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 -105 -104 -103 -102 -101 -100 -99 -98 -97

A23
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 -44 -43 -42 -41 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 -105 -104 -103 -102 -101 -100 -99 -98 -97

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GRIMM 2.01 by Glenn Tesler, University of California, San Diego.
Copyright © 2001-2006, The University of California.
Contains code from GRAPPA, © 2000-2001, The University of New Mexico and The University of Texas at Austin.

MGR 1.36 by Guillaume Bourque (now moved to McGill).
Copyright © 2001-2005.
Contains code from Phylip 3.5, Copyright © 1986-1995 by Joseph Felsenstein and the University of Washington.

Click here for details on how to cite this in your work.