top of page

How to upload a project to PhyloJIVE (ALA version)

Uploading a new project to PhyloJIVE at the ALA

Go to the ALA and make a user account and login
To start navigate to the PhyloJIVE ALA webpage
http://phylojive.ala.org.au/
 

Select Case Study 1: Acacia and play around and see how it works
Refer to here  for navigating instructions

Don't forget to click on upload Load Characters via IdentifyLife

 

​​
Click on create a new tree in the upper right hand corner
Give the project a name

 We have not yet implemented a filing system for projects
All that is required to use PhyloJIVE is a newick tree file
 Paste in a newick tree file in the designated box. It has to be a single line of text, without headers or returns.  Please delete any ' or " in the text. See demo dataset which is ready to paste in the box.  Acacia_tree.txt

​In order to access the mapping and webservices links from the terminals PhyloJIVE has to be able to recognize the binomial names, such as Acacia dealbata, on the tree 

   

​

​User defined trait data can be uploaded and mapped to the phylogenetic tree.  This is not a requirement.
 Please see the Acacia.csv file for formatting information.
 Traits can be either in charJSON or in a .csv file.
     charJSON is explained in paper to be submitted soon

​

How to do it 

​

Place data in a .csv file

  •  See example file Acacia.csv​

  •  First column should be the species binomial with the name matching the exactly matching tree

  1.  Order is not important

  2. The number of taxa can be different than in the tree

  3.  Missing data is ok

  •  The rest of the columns are characters states with the top row used for the character name

  1.  You can mix quantitative and qualitative characters

  2.  Maximum number of characters depends of browser, start small

  • If there the termnalhas more than two character states you need to use a separator such as (& or %) between the character states in the cell

  1.  You need to specify this separator in the upload page

  • Save file as .csv and open it in notepad (not excel)

• Copy and paste it into the window


• Click convert to charJSON

  1.     Include separator if necessary

  • Please write a little in the attribution, keep it public for now so I can help

  • Currently we have access only to the Australian Acacia dataset in IdentifyLife

  1. We hope to access more external trait datasets in the future

  2.  Write acacia if you  dataset contains Acacia species

  •   Click CREATE

  • Click on the link to the page


Email Joe Miller or Garry Jolley-Rogers if you have issues or if it works.  We would like to know.  We also welcome any feedback, especially to our instructions.



joe@acaciamulga.net
garry.jolleyrogers@gmail.com

bottom of page