Vrml Mod

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Below is the spec for the multiple alignment animation generator 'vrmlmod.' (You can find the code from here; it's also part of DART.)

Vrmlmod's main purpose is to provide a graphical means of examining the evolutionary history of multiple alignments. Here is a contrived example of the input and output of the program:

NAME: vrmlmod

USAGE: from within directory:

./vrml [options] [input] [output]

DESCRIPTION: Vrmlmod writes to output a vrml file (*.wrl) modeling the phylogenetic tree embedded in the input Stockholm format multiple alignment. All branches of the tree (including inner nodes) must be named and present in input, both in the alignment and in the newick representation of the tree. The resulting output file can be viewed using a VRML browser. (note - vrmlmod was developed using Cortona's VRML client ) Alignments longer than 100 basepairs long are scaled down to a default size of 50 and a difference- based color scheme is used rather than a basepair-to-color mapping. In a scaled display, glowing elements represent quickly evolving portions of the alignment where in a full display, they represent changed basepairs.


  • -a : ancestor comparison : In full display, compare sequences to root rather than parent for glow markup. In scaled display, compare sequences to parent rather than root for color-mapping and glow markup
  • -b : background : Toggles a more interesting background (default is black)
  • -f : force full display : Overrides default scaling of alignments longer than 100 basepairs
  • -r : rotation : Disables rotation in evolution animation
  • -s : side view : Sets side-view as final viewpoing
  • -t NUM : time scale : Accelerates the timing of the evolution animation by NUM which is limited to 0 < NUM <= 10
  • -v : viewpoint switch : Enables switching of the viewpoint during evolution animation
  • -x NUM : scale size : Sets the scaled display element map to NUM elements (default is 50). Because of viewpoint limitations, NUM is limited to 10 <= NUM <= 500
  • -z NUM : spacing : Decreases element size and increases branch lengths by NUM to space out large phylogenies. Because of viewpoint limitations, NUM is limited to 0 <= NUM < 5


  • Because of the nature of Cortona's browser and many other browsers, starting positions and viewpoints are variable when refreshing VRML. Also, Cortona's mac browser does not support text. (Made it difficult to develop a standard for displaying text)
  • The arcs in an RNA alignment model represent matching base pairs and the consensus secondary structure given in input.

-- Kenny Duong - 11 Aug 2005