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Phylogenetic Tree (0.1)

by Ihor Berehulyak last modified 2009-01-13
Released on 2005-08-22 by Jeff Pittman for Plone 2.0 under GPL - GNU General Public License available for All platforms.
Software development stage: alpha
PhylogeneticTree draws "evolutionary tree" diagrams for representing the evolutionary history of a group of organisms. PhylogeneticTree focuses on the standard cladogram, skewed right, showing branches and nodes of the tree spreading from lower left, and with the taxon names (organism, or organism group names) arrayed across the top in the leaf positions. The program is primarily designed for web presentation of known cladograms. It has its own simple data design treating the cladogram as having a given number of rows, which lie vertically between levels of the nodes, and columns, which are the lateral internode spacings. Input includes a few settings for the layout of the diagram and the main data, which includes two data series in CSV format: one for the character and character descriptions and the other for the node descriptions. Node descriptions require the user to draw an existing cladogram on graph paper to gather data for row and column position of the nodes. Once you have learned the data format, specification of node data is straightforward.

PhylogeneticTree uses the ReportLab toolkit to generate a phylogenetic tree plot and its own routines to emit SVG and simple HTML renderings.

PhylogeneticTree is a folderish Archetypes-based Plone/Zope product. The idea is to use various renderers to create images, PDF files, and/or SVG versions of the cladogram and store them. This allows flexibility for a user of PhylogeneticTree to offer several format versions, if needed. PhylogeneticTree takes input of the following items:

Javascript tooltips are used to show short descriptions of characters when the user mouses over a node.

  • row height (vertical internode spacing, in pixels)
  • column width (lateral internode spacing, in pixels)
  • characters, entered as comma-separated values on separate lines. Characters are specified by:
    • character number (for easy reference in the node descriptions)
    • short description
    • long description
  • nodes, entered as comma-separated values on separate lines. Nodes are specified by:
    • parent (taxon name of parent)
    • taxon name
    • characters (entered like this, by character number: [1,2,4,9])
    • row position
    • column position
    • font size
    • line style (solid, dashed)
    • line base style (connected, gapped)
    • line stroke width
    • branch direction (root, left, up, right)
    • line color (line_red, line_green, line_blue (each 0-255)
    • node style (circle_solid, circle_open, square_solid, square_open)
    • node size (in pixels)
    • node skew (angle, negative for left, 0 for up, positive for right)
    • node color (node_red, node_green, node_blue (each 0-255)
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