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getting started darwin sketch

with phyloJIVE and your own data

   for developers,   wiki instructions + known problems,   download phyloJIVE  

Download this project as a .zip file Download this project as a tar.gz file

Quick Start Template... for the impatient

This simple template provides a minimal set of features.  The file structure in the folder containing this template can be used to set-up your own  instance of PhyloJIVE on your desktop or embedded in a webpage.  For more details, see the phyloJIVE web application parameters page.

There are two ways to change the data.  

  1. First you can click the ipad-like button at the top, click on the Input tab and paste a newick tree in the box and clickon Render.  You cannot input trait data with this method.

  2. The second way utilizes the file structure.
    1.   Parameters, trees and characters can be altered by editing SimpleParams_PhyloJIVE.js Open SimpleParams_PhyloJIVE.js in the trees_character folder.   This file contains the data that you can view on the right of this screen, i.e. the tree and character data. 
      There is also a blank template.js.
    2. Simply paste the new tree over the old making sure the  punctuation is maintained.   Should a large newick tree fail to display then the first thing to check for is escape characters such as quotes for informal names or unnamed specimens.
      The character trait data can be updated by first converting a csv file to charJson by using the supplied converter
    3. Then paste the  charJSON formatted character data over the data in SimpleParams_PhyloJIVE.js.  located in the trees_characters folder
      Character sets can be either qualitative or quantitative or a mix of both types.


If you wish a more appropriate name for the file which contains trees and characters or you have more than one tree. You simply need to edit the html file to replace the reference to SimpleParams_PhyloJIVE.js. A text view of the html file is shown here.

what to change if you want to rename to file containg
          trees and chars

Changing external links - using templates<<< Reccomended

Two examples of how to change the external links using the link template
Australian extent endemic birds and Amphibia.  Details of the syntax are on the parameter page.

Punctuation (syntax) is important. Commas, brackets and braces must match. They should remain
            example of a templated list

Changing external links- over riding the presentClade function <<< The hard way

More exquisite control can be achieved if you over ride the presentClade function. This is done by including a new definition of it on initialization as seen in Syncarida .
an example of how to override the presentClade

Changing what appears on hover (the tips function)

  Syncarida  shows how to change what appears as the mouse hovers over a taxon or clade.

You  need to override the tips function.
This is done by creating a new one which  is saved with the tree and other initialization variables. 

A screen grab showing how to override the tips

 GUID's (LSIDs) 

An example where GUIDs are used (Syncarida plus LSIDs). Taxon names are looked up with a nomenclator then  translated to the equivalent LSID.

Strictly speaking any GUID's should be supplied with the phylogeny Or the creator of the phylogeny should explicitly state that they are using the  taxon concepts as recorded in a particular source at a particular time. However, such perfection is rarely attainable. This template is provided as a proof of concept.