Phylemon2 offers a set of new tools:

• to align sequences:
  • Lagan
  • M-Lagan
• to straightly build phylogenies
  • PhyML Best AIC tree
• to test for best evolutionary models:
  • jModeTest
• to visualize trees:
  • Archeopteryx

Other tools in Phylemon are not exactly new to the server but suffered consequent changes, here is a list of the major improvements:

• phylogenies
  • MrBayes: added the ability to run it non-interactively, and also to build command block by selecting options in a form.
• Evolutionary tests
  • ProtTest: upgrade to new version (now HYPHY independent) and added ability to upload a “user tree”
• to edit/visualize trees
  • ETE (the tool was already present in previous version of phylemon, but only as viewer)

Those are the main upgrades, but users will notice changes in nearly all the tools in Phylemon2.0 due firstly to upgrades to their last version but also to a more complete selection of examples and better organization of the forms.

In this new version of Phylemon, a special attention was paid to project and job management. Users can now easily rename or delete projects and jobs. Also separation between Projects and Data may help users to find quickly the exact file/job.

In order to limit errors related to bad inputs, user is now asked to label each file uploaded. This feature may be considered as tedious by new users, but has been thought to force selection of right kind of file (e.g.: user will not be allowed to load a file labeled as tree when an alignment is expected), and also to ease the finding of the wanted file (see picture bellow, in this example Muscle stipulated that only files of type “alignment” and “non-alignment” can be used, files not labeled with those terms will appear in gray).

File generated by the tools in Phylemon will also be labeled, this time, automatically.

User can get start with project and data management by following the Trial on my first prject.

Also the pipeliner tool is not new in Phylemon, in previous version (called “SuperPhylemon Pipeliner”), very few tools were compatible with it (ClustalW to align, some of PHYLIP package and ETE to see a static image of the tree).

In this version of Phylemon the pipeliner was entirely rewritten, and proposes a extended selection of tools that will finally allow user to work on hundreds of alignments (see pipeliner description for more details).

Those new features in combination with the eased project management presented above, makes Phylemon be one of the most easy way to do phylogenomic analysis.

This wiki is also new, its first purpose is to complete the information provided by the designers of the tools in Phylemon (usually accessible through Help link for each tool), that would be the Tool description section.

But also propose some exercises, based on our teaching experience, that are designed for users new to phylogenetic analysis, and would familiarize them to the most common/relevant options.

Also some trials (see My first project, or Trial on My first project) and FAQs were written for users new to Phylemon.

Phylemon has been entirely rewritten, and on top of the above mentioned enhancements, user will find some extra features as the Left side bar for job notifications and quick links, the internal job management (now done though Oracle Grid Engine) that ensure each job to be fairly distributed in our cluster (see Web cluster stats, on the top of Phylemon page), Citation link is now visible from most tools to copy bibliographical references…

Finally we would mention the contact form that was built in order to allow users to easily and precisely report problems or send us suggestions.

Phylemon team is listening, please feel free to send propositions and feedback