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

© 2018 by Joe Miller.