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Last Update : 3 March 2006

Phylojava is a client/server tool dedicated to phylogenetic tree reconstruction. This program allows phylogenetic tree inferences according to most usual methods (distance methods, maximum parsimony, maximum likelihood). Phylogenetic trees are computed on a remote server, and are sent via internet to a graphical interface (the client) that allows the user to handle alignments and phylogenetic trees. The user therefore only has to install the graphical interface on his computer, and can submit tree reconstruction jobs on a remote server. Default phylojava server is the one installed at the Pôle Bionformatique Lyonnais (PBIL).The PBIL address for your phylojava client is :
You can get the list of all phylojava servers by clicking on the "server" menu and change your server by copy/paste the address.

Use of Phylojava

Taxonomic species groups and sets of conserved regions can be defined using mouse and stored into sequence files, thus avoiding multiple data files. The program is entirely mouse-driven. An help menu explains more in details how to use the application and methods description. You can also find phylojava help here.
Most usual sequence file formats in phylogeny can be read: CLUSTAL, FASTA, MSF, PHYLIP and MASE.
A screen shot of the main window is available here.

Phylojava server

In order to set your own phylogenetic methods, you can freely install a phylojava server in your laboratory. New methods could be easily added writing an HTML form and a script that will launch the algorithm with the correct parameters. The execution of phylogenetic methods rely on a Common Gateway interface (CGI) through an HTTP server. Therefore you need a running HTTP server and a Open Portable Batch System (OpenPBS) installed in order to queue long jobs whereas short jobs will be directly executed and results sended to the client.


A special set of methods can parallelize maximum likelihood jobs on Datagrid environment. It affords to use computer resources of several computer center accross Europe.
Please, ask Laurent DURET if you want to use it.

Calculation center IN2P3

The PBIL server can switch a part of the CPU workload to the IN2P3 calculation center. We have a privilege access to the center that is one of the major nodes of the grid. Info to obtain an account and how to use the resources : manual.pdf (in french)

Download Phylojava

Phylojava is still under development. Please comme back later.
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