Frequently asked questions (FAQ)
If you use PhyleasProg for your analyses please cite:
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W479-85. Epub 2011 Apr 29.
PhyleasProg: a user-oriented web server for wide evolutionary analyses.
Busset J, Cabau C, Meslin C, Pascal G. free full text.
Be sure that your query IDs are Ensembl protein IDs:
No, PhyleasProg supports only protein IDs from Ensembl database as query. Nevertheless, you have the possibility to search for an orthologous sequence of your gene in Ensembl database and to submit it to PhyleasProg. However, future releases of the program will soon include the possibility to submit user's own sequences.
To choose orthologous genes, PhyleasProg uses the same pairwise relationships as Ensembl. To see a description of these relationships, please visit the Homology types section. When orthologs are of type ortholog_one2many or ortholog_many2many, the longest orthologs are chosen.
Results of PAML computation with site models are available only if the LRT comparison between the log likelihood of the two compared models is significant.
To access to results of calculations with branch-site models, you have to click on branches of the phylogenetic tree. If the branch is under positive selection, it will be highlighted in green.
On this page, you can see the sequence of the protein ADRO from cow with highlighted amino acids. The color of the highlighting depends on the value of the ω ratio for purifying selection (green scale) and on the value of posterior probabilities p for positive selection (red scale). In white, no information is available because no calculations were performed by codeml because of a gap in the multiple sequence alignment. In grey, results are not enough significant to infer neither purifying nor positive selection. The same color code is used on the 3D structure displayed by Jmol.
The multiple sequence alignment used for PAML computation is also viewable, displayed by JalView.
If there are stretches of gaps in alignment between your protein and the PDB used as a template to model with Modeller, the resulting structure can be truncated into 5' and/or 3'. A message will inform you above the alignment on your result page if it is the case.
PhyleasProg shows results on a 3D structure if a 3D structure can be modeled with Modeller from a sequence of the PDB database. If the alignment between protein from PDB and pivot protein is not conclusive, results are only presented on the 1D sequence.
Files that can be downloaded are available in the flat files section of the results page. Moreover, all result (rst) files of the PAML computations can be also downloaded.
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