About Phylogenomics

Phylemon's Pipeliner is a tool designed for enabling users to develop their own pipelines in a friendly modular environment allowing you to run multiple gene or phylogenomic analyses using multiple programs. Designed pipelines can be saved either to your machine or in phylemon server and loaded in the same way. Once designed they can be used to repeat the set of analyses on other sets of genes.

To load one tool on the pipeliner main area, select it from the left side bar. A node figuring the tool you selected will appear on the field.

The tools available in the pipeliner are:

• Alignment
  • ClustalW
  • Muscle
  • Trimal
  • Cds-Protal
• Phylogeny
  • DnaDist
  • ProtDist
  • Neighbor
  • Fitch
  • SeqBoot
  • Consense
  • PhyML
  • PhyMLBestAICTree
• Viewers
  • ETE

Plus a tool named Phylogenomics that allows you to upload multiple files as described below.

A short description of each tool is available on “mouse-over” (up right corner of pipeliner field).

In order to take the output from one tool as input of another the user will have to activate the “Create link” feature, by clicking on the corresponding section in the menu. Afterwards The user should click consecutively on the source node and on the target node. A message should appear on the right part of the pipeliner application, before selecting the first tool: Select source node, and after Select target node.

Once the pipeline is built, the user should revise all the forms of each tool, and select the appropriate parameters.

In order to ease the organization of jobs and data, each run of the pipeliner is associated to a new project taking the default name of “Pipeline_1” if not set.

When the “Run” button is pressed, working project will automatically be changed to “Pipeline_1” if not changed. To get back to your favorite project, go to the project manager and select it.

When all steps above are completed, and infiles are loaded, the user could be able to execute the pipeline. To do so just click on “Run”, each one of the job will be appearing in the phylemon right side bar as they reach the queue.

Jobs will be executed one by one.

In order to keep the structure of you pipeline you can save it to phylemon just as a data file.

Once saved on the server you will be able to download it to your computer also (this feature is practical to share your pipeline with other people).

This tools allow the user to load multiple data. The user should select on his computer the input files (of the same type, alignments, trees, distance matrices) and compress them. Compression format should be Zip.

Phylogenomics tool will uncompress the input files and send them to the next tools.