FAQ
How do I cite PhylomeDB?
Please cite PhylomeDB each time you have used it for
your published research. Either if you downloaded a whole dataset or
whether it was the source for obtaining some relevant evolutionary information,
or the sequences to prime some phylogenetic analysis. Cite the most recent
publication of the database, which is now v5:
PhylomeDB V5: an expanding repository for
genome-wide catalogues of annotated gene phylogenies.Diego Fuentes, Manuel Molina, Uciel
Chorostecki, Salvador Capella-Gutiérrez, Marina Marcet-Houben, Toni Gabaldón Nucleic Acids Research. Volume 50, Issue D1, 7
January 2022:D1062–D1068. doi: 10.1093/nar/gkab966.
If you want to refer to the phylogenetic pipeline used in PhylomeDB, which was described in
v3 paper, please cite:
PhylomeDB
v3.0: an expanding
repository of genome-wide collections of
trees, alignments and phylogeny-based
orthology and paralogy predictions. Huerta-Cepas J,
Capella-Gutierrez S, Pryszcz LP, Denisov I, Kormes D,
Marcet-Houben M, Gabaldón T. Nucleic
Acids Res. 2011 Jan;39(Database issue):D556-60.
I have
a phyID, what can I do with it?
phyID's are
numbers associated to phylomes. They are usually provided
in the phylome publication and are useful to quickly pick
out the phylome of interest from the complete list of phylomes.
phyIDs can be found in the All phylomes tab, as
the number located next to the phylome name. They can also be used to
locate the download data within the ftp repository where phylomes are
identified only by their phyID (Downloads --> phylomes -->
phylome_+phyID).
Alignments are not displayed
properly in my browser
PhylomeDB uses Jalview,
an external application that
requires Java. Please, check that you
have the latest version of Java
installed and that Java is enabled in your
browser. When correctly installed your
browser should display the following
target="_blank" class="urlextern" href="http://www.jalview.org/examples/applets.html">examples
properly.
You can
download the latest
version of Java at
class="urlextern" href="http://www.jalview.org/examples/applets.html">Java
Download
Site.
What type of branch supports are used in the phylome?
The specific methods used for each phylome are explained in the corresponding “phylome information page”. Due to computational and time constrains, for most phylomes we did not used standard bootstrap analyses. Instead we usually compute approximate Likelihood Ratio Tests (aLRT), as implemented in
target="_blank" class="urlextern" href="http://www.atgc-montpellier.fr/phyml/versions.php">PhyML-aLRT
or in
class="urlextern" href="http://www.atgc-montpellier.fr/phyml/versions.php">PhyML
v3.0 version.
When I press "show branch
support" icon, not all branches
display the support
When you press the “branch support” icon, red numbers with the support values will appear beneath the branches. If some do not appear it is because there is no space to show the number, in that case you can press “force topology” and all branch lengths will be re-sized to display all supports.
What do the
different branch colors
indicate?
Red
indicates branches in which our species-overlap algorithm detects a
duplication event, whereas
speciation events are marked in blue.
This color-coding system coincides to that used in EnsemblCompara trees.
What are "collateral trees", what are
they useful for?
Collateral trees of a given protein are those trees in which that protein is present but it was not used as a
seed for the tree reconstruction. In other words, they are trees for which a paralog of the given protein was used as a seed. Collateral trees
may provide additional information on the topological position of a given protein. If several collateral trees support a specific relationship
(e.g an orthology relationship or a duplication), we can regard this as additional evidence for that relationship.
Collateral trees also provide information about proteins that belong to an organism that has not been used as seed in any phylome but is
present in them.
I cannot find a tree
for a given protein, even if the protein is present in
the proteome you used to build the phylome
For sequences that did not produce at least three significant hits in the
genomes considered (see the specific parameters and cut-offs in the phylome information
page) we cannot reconstruct a tree. This is probably the reason why you cannot find a tree for these sequences.
I want to
add some additional sequences (from
a species not included in the phylome)
and re-do the tree using the same
parameters. How should I proceed?
Click on the "download data.tar.gz" button on the top of the tree
visualization pannel. This will download a compressed folder with several
files in it. There you will find a multi-fasta file with all the sequences
(file ended by .msf.fasta) and the raw alignment file (file ended by
alg.raw.AA.fasta). Then, you can align your sequence to the alignment.
Muscle or Mafft have options to directly align sequences to an pre-existing
alignment. Alternatively you can just add your sequences to the multifasta
file, re-align with MUSCLE, trim with trimAl and build the tree with PhyML,
with the parameters indicated in the phylome information page. All these
programs can be downloaded or are available through the
href="http://phylemon.bioinfo.cipf.es">Phylemon
webserver.
I want to create a direct link from a
webapge to phylomeDB resources/results. How
should I proceed?
You can find the information at the User's manual section:
How to link to phylomeDB.
You have a lot of possibilities to link the resources such as the
information about a specific phylome or the results for a given query
such as phylogenetic tree for a protein in a specific phylome, etc
I want to use the PhylomeDB tree image for a publication but the one in
the website does not have enough resolution. How should I proceed?
You can download a
high resolution version of the image in .svg format.
This file is provided together with other data when
downloading the data associated to this tree. You can do
this by clicking on the "download tar.gz" button of your
favorite tree. You should be able to open that image with
several image editors and modified at wish.
I
find several proteins with identical IDs in the same tree. What
are these?
These sequences correspond to different
genes in the same genome that encode identical proteins. As Uniprot
does, we assign the same protein identifier for to all proteins within a
single species that are identical in sequence. These sequences are usually
very recent duplicates (perhaps CNVs) that did not diverged yet at the
protein level, or genes that are undergoing gene conversion.
Phylo Explorer does not responde to any input. What happened?
Phylo Explorer is mainly built in the Javascript programming language, which is
dependent on the browser's version.
Updating your browser to the latest release should solve the problem. If that is not the case, contact with our
maintenance.
Phylo Explorer has lag issues, when the mouse cursor moves on the heatmap.
Phylo Explorer to serve useful information, must import large amount of data from
the database and manipulate them locally, so the performance depends on the user's system. Try adding more
species to the combination in the principal page of Phylo Explorer, or using the filter search bar above the
heatmap to narrow down the displayed result.