Trial on MyFirstProject

Lets have a quick insight of job/project management with our trial project MyFirstProject (c.f. My first project section).

The topic of this trial will be, starting from not-aligned sequences, to compute distances, solve a phylogeny and finally draw a tree.

For this step we will use the Muscle software (Alignment → Muscle (version x.x)).

As with any of the tool/utility proposed by Phylemon, we can access to the documentation page of this tools through the Help link. Also it is possible to see the reference of the article corresponding to the current tool (if published).

Each one of the tool/Utility in Phylemon can be launched with at least one example, in this trial we will use the example in muscle, an alignment in FASTA format of p53's nucleotidic sequence of some vertebrates. To load the example file, just expand the example menu, and fill in form with desired example.

When an example is load, it is common to see change in the default options, those changes correspond to to what we think would be the best for running it, but user can still modify them. If you agree with the selection of parameters, just go straight to the run button, and apply our first job.

To load your own sequences by clicking on “browse server” button and selecting “Upload new file” you will be asked to choose a “tag” for each file you upload, or you can also paste directly your data in the text area below: “Or enter your data from text” (cf: blue arrows in previous snapshot).

Once applied our job appears in your job list on the side bar as queued job (orange). Your job will be labeled as running when Phylemon's server will start computation and finally, will appear in green and be labeled as finished while they still unvisited.

Job queued	Job running	Job list finished	Data list finished

You can also see the progress (same color code) of your jobs at the Projects page (). Before having a look to our output lets change the default name given by Phylemon to our job. Go the the Projects page and click on the little in front of your job.

Now we can have a look to the output by clicking on our new name: My first alignment. (Note that it will turn purple as “visited job” once seen)

Our alignment file can be downloaded by clicking on the alignment file link muscle.fasta.out. This file will now be stored in your Data you will be reachable from through or through your “Data list” view in the left side bar.

You can also have a quick look to the file inside your browser just by extending/collapsing the “view” section (usually this view appears collapsed).

Other actions are available at the bottom of each result page:

• Open input form to use again the same tool with other parameters, or just have a look to them.
• Download job to get the job and all its dependencies as zip file.
• Submit an error

We now have an alignment of our sequences and want to compute the distances with DnaDist. Select “Send to DnaDist tool” and click on “Send”.

We are now in the DnaDist page, with our input file already loaded (muscle.fasta.out) and the different parameters set to default. We can change them for a more specific computation (again information of the different options available can be found through the Help link). For this trial lets just name our job “Trial p53 DnaDist” and click on “run”.

This time, we already named our job in our convenience and can go directly to the output, so once the job name turn green, just click on it.

If we expand the output (also available for download as text file through the outfile link), we should see the distance matrix corresponding to our alignment.

For the next step, and in order to finally obtain a tree, redirect this distance matrix to the Neighbor tool also from PHYLIP package.

At this step we should have a distance Matrix corresponding to the alignment of some p53 sequences. If we go to the corresponding output page we can directly send this distance matrix as input file to the Neigbhor software.

Here again we can let all parameters by default, just complete the Job name box with in example “Trial_p53_Neighbor”.

and click on “Run”.

Have a look to the outfile (human readable text file), and send outree file to ETE for visualization of the tree.

Go to the output of Neigbhor and send it as input to ETE. Try to use it to draw a rectangular tree, and, afterwards re-run it to obtain a radial tree, and changing image size to obtain the desired tree image.

And have a look to the interactive tree generated:

You can play with the different layouts by clicking on the background, swap/collapse/highlight part of the tree by clicking on internal nodes (more options are available for leaves) etc… But be careful with option with red letter they may be irreversible, and last version of your tree will be saved in out file

You have now obtained your trees from your p53 sequences. You can now have a look to you projects and data.

Lets go to your Projects page (). Here you have in chronological inverse order, all the jobs you run under your different projects. All the files you used and generated are here stored, and, as you will be able to use them in different analysis, it is use full to name them in a meaningful way.

This view is under the Tree view (not the default).

In the Data page () you will find all the data generated by your jobs. This data is also tagged and reachable from every tool (“Browse server” → “Job generated”).