Phylogenetic Analysis Programs
v3.1
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Quick guide



How can I start PhyleasProg?

To run PhyleasProg, you just have to paste your Ensembl protein IDs, to choose all species or your species of interest, to select your level of computation (fast or fine), to choose to run PhyleasProg on orthologs or on both orthologs and paralogs and to click on "Start computation" button. You can supply an email address to keep a trace of the results page URL. On the next page, you will see a recap of your request. If it is not correct, you have the possibility to change it or you can confirm it to really start the computation. Due to technical constraints, jobs are limited for now to 20 query IDs.


How can I explore my results?

Job summary page

On this page, you can consult the status of the PhyleasProg computation (queuing, running or finished). You will also find links to all PhyleasProg results for each protein ID of your request and the list of selected species for the job. One the left, you find links to results page for each protein ID.


A sample page of results



Legend

With this link, you will access to all results concerning orthologous gene of your query ID.
With one of these links, you will access to all results concerning each set of paralogous gene of your query ID.
With one of these links, you will access to all results concerning orthologous gene of the others IDs of the same job.
You will access to the phylogenetic tree of your gene, displayed by Archaeopteryx.
You will access to the result of positive selection calculations, with site models and to result (rst) files of codeml.
You will access to the result of positive selection calculations, with branch-site models. Results are shown on a clickable tree; branches under positive selection are represented by a purple star and are highlighted in green. Result (rst) files of codeml are also available.
You will access the Genomicus page of your gene. To get more information about the Genomicus browser, please visit Genomicus website.
This section lists all important information about PhyleasProg computation (removed sequences, impossibility to find orthologs in such and such species, etc.).
In this section, you can find and download flat files (sequences, multiple sequence alignment, 3D protein structures, phylogenetic tree).


Results of selection pressure with Branch-Site model


Results of PAML computations with Branch-site models are presented on a clickable tree. Significant results are indicated on nodes by a purple * or for external branches, names of the sequences are indicated in purple. For this example, the branches of the common ancestors between human, chimpanzee and macaque, highlighted in green on this view, is under positive selection. Branch of xenope is also under positive selection.

If you click on the branch highlighted in green on the previous image, you can choose from the dropdown menu the sequence for which you want the results displayed, here the human, chimpanzee or macaque. The 1D sequence will be the one selected in the dropdown menu and the 3D sequence displayed by Jmol will be the modeled structure resulting from Modeller computation.