The server is still under development. It will be operational soon.
Please come back later.
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
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
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)
Phylojava is still under development. Please comme back later.
If you have problems or comments...
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