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

Sankoff et al., 1996 analyzed human, sea urchin, and fruit fly mtDNA to derive the ancestral gene order. Click here for details.

Tree recovered (Newick Standard)

(Humans:7,Fruit Fly:15,Sea Urchin:17)A3;

Score: 39 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

  +-----------7------------Humans
  |  
  |  +------------------------15---------------------------Fruit Fly
  +-A3  
     +----------------------------17------------------------------Sea Urchin

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)


  Humans Sea Urchin Fruit Fly
Humans 0 24 19
Sea Urchin 24 0 32
Fruit Fly 19 32 0

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

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

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

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

A3
26 13 17 12 -24 15 18 32 25 22 11 29 14 5 1 10 19 -2 -3 -33 4 -28 7 -6 21 -20 -16 8 30 -23 9 27 31

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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.