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:
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MGR Report

Blanchette et al., 1999 used BPAnalysis in the rearrangement study of 11 metazoan mtDNAs. Click here for details.

Tree recovered (Newick Standard)

(Ascaris suum:15,((((Cepaea nemoralis:5,Albinaria coerulea:2)A17:23,Lumbricus terrestris:6)A16:10,Katharina tunicata:6)A15:5,((((Paracentrotus lividus:0,Asterina pectinifera:1)A11:17,Human:7)A12:15,Drosophila yakuba:0)A13:1,Artemia franciscana:2)A14:7)A18:21,Onchocerca volvulus:7)A19;

Score: 150 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

  +--15-----Ascaris suum
  |  
  |                                              +5-Cepaea nemoralis
  |                             +-----23-------A17  
  |                      +10--A16                +2-Albinaria coerulea
  |                      |      |  
  |                  +5A15      +-6-Lumbricus terrestris
  |                  |   |  
  |                  |   +6-Katharina tunicata
  |                  |  
  |                  |                               +-Paracentrotus lividus
  |  +-----21------A18                  +---17-----A11  
  |  |               |       +--15----A12            +1-Asterina pectinifera
  |  |               |       |          |  
  |  |               |    +1A13         +-7-Human
  +A19               |    |  |  
     |               +-7A14  +-Drosophila yakuba
     |                    |  
     |                    +2-Artemia franciscana
     |  
     +-7-Onchocerca volvulus

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)


  Human Asterina pectinifera Paracentrotus lividus Drosophila yakuba Artemia franciscana Albinaria coerulea Cepaea nemoralis Katharina tunicata Lumbricus terrestris Ascaris suum Onchocerca volvulus
Human 0 25 24 19 22 33 34 28 30 34 35
Asterina pectinifera 25 0 1 32 32 31 32 31 31 33 33
Paracentrotus lividus 24 1 0 32 32 32 31 32 30 34 34
Drosophila yakuba 19 32 32 0 3 32 33 19 26 34 33
Artemia franciscana 22 32 32 3 0 31 32 20 25 34 33
Albinaria coerulea 33 31 32 32 31 0 7 31 31 34 33
Cepaea nemoralis 34 32 31 33 32 7 0 33 31 34 34
Katharina tunicata 28 31 32 19 20 31 33 0 22 32 30
Lumbricus terrestris 30 31 30 26 25 31 31 22 0 31 31
Ascaris suum 34 33 34 34 34 34 34 32 31 0 21
Onchocerca volvulus 35 33 34 33 33 33 34 30 31 21 0

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

Human
1 -32 17 2 23 12 3 20 6 30 7 8 21 31 24 9 -10 -18 11 33 -28 19 14 34 13 25 4 22 -29 26 5 35 -15 -27 -16 -36

Asterina pectinifera
1 30 7 2 23 12 3 -32 6 8 21 31 9 -10 11 19 14 18 33 -13 -5 -22 -4 -25 -20 -36 17 -26 34 -16 -35 15 -24 -27 29 -28

Paracentrotus lividus
1 30 7 2 23 12 3 -32 6 8 21 31 9 -10 11 19 14 18 33 28 -29 27 24 -15 35 16 -34 26 -17 36 20 25 4 22 5 13

Drosophila yakuba
1 25 2 23 17 12 3 20 6 15 30 27 31 18 -19 -9 -21 -8 -7 33 -28 10 11 32 -4 -24 -13 -34 -14 22 -29 26 5 35 -16 -36

Artemia franciscana
1 25 2 23 17 12 3 20 6 15 30 27 31 18 -19 -9 -21 -8 -7 33 -28 10 11 32 -4 -24 -13 -34 -14 26 5 35 -22 -29 -16 -36

Albinaria coerulea
1 34 13 24 28 15 10 9 4 7 11 17 16 19 2 36 35 20 21 -29 -25 -27 -12 -30 -18 -14 -26 -6 -32 31 8 -33 -3 22 5 23

Cepaea nemoralis
1 34 13 24 15 10 28 9 4 7 11 17 16 19 2 36 35 20 21 -29 -25 -27 -12 -30 -18 -14 26 -6 -32 -33 -3 31 8 22 5 23

Katharina tunicata
1 17 2 12 -19 -9 -21 -8 -7 33 -32 -11 -10 28 -4 -25 -24 -13 -34 -14 -26 -16 -36 -35 -29 -20 -18 3 23 15 30 27 22 6 31 5

Lumbricus terrestris
1 27 2 17 36 20 3 29 10 11 35 12 30 21 9 19 18 28 33 7 8 16 26 14 34 13 24 15 32 25 4 22 23 6 31 5

Ascaris suum
1 16 26 17 20 2 21 13 6 9 15 28 34 10 7 35 18 14 32 27 36 4 12 23 25 31 5 22 30 29 19 11 24 3 33 8

Onchocerca volvulus
1 35 10 30 29 11 24 3 23 15 25 27 26 7 14 36 4 19 12 22 20 2 21 13 6 16 32 28 17 34 9 18 31 5 33 8

A11
1 30 7 2 23 12 3 -32 6 8 21 31 9 -10 11 19 14 18 33 28 -29 27 24 -15 35 16 -34 26 -17 36 20 25 4 22 5 13

A12
1 -32 17 -11 10 -9 -27 18 33 -28 19 14 34 13 25 4 22 -29 26 5 35 30 7 8 21 31 24 2 23 12 3 20 6 -15 -16 -36

A13
1 25 2 23 17 12 3 20 6 15 30 27 31 18 -19 -9 -21 -8 -7 33 -28 10 11 32 -4 -24 -13 -34 -14 22 -29 26 5 35 -16 -36

A14
1 25 2 23 17 12 3 20 6 15 30 27 31 18 -19 -9 -21 -8 -7 33 -28 10 11 32 -4 -24 -13 -34 -14 22 29 26 5 35 -16 -36

A15
1 17 12 -19 -9 -21 -8 -7 33 -28 10 11 32 -4 -25 -23 -3 18 22 29 35 36 16 26 14 34 13 24 15 30 27 2 20 6 31 5

A16
1 27 2 20 -4 -25 -23 -22 3 29 -18 -19 -9 -21 -8 -7 -33 -28 10 11 35 36 17 12 30 16 26 14 34 13 24 15 32 6 31 5

A17
1 34 13 24 15 10 9 4 7 11 17 16 19 2 36 35 20 21 -29 -25 -27 -12 -30 -18 -14 -26 -6 -32 31 8 -33 -28 -3 22 5 23

A18
1 25 31 5 -35 -29 -22 -12 -17 -23 -3 14 34 13 24 15 30 27 2 20 6 4 -32 -11 -10 28 -33 7 8 21 9 19 -18 -26 -16 -36

A19
1 -32 -27 -18 -35 28 17 -22 -12 -19 -29 -30 -10 -9 -34 20 2 21 13 6 16 26 7 -23 -3 -24 -11 -4 -36 -14 15 25 31 5 33 8

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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.