PhylomeDB User's Manual Index
Main Tree Page
The tree interface is the central feature of phylomeDB. The tree is fully interactive and can be manipulated as well as used in order to obtain additional information. Clicking on different parts of the tree will produce drop-down menus through which a tree can be manipulated. The default tree shown after a search belongs the most recently reconstructed phylome and the best evolutionary model within this phylome. You can change the tree selection using the menu placed just on top of the tree.
The features explained below will allow you to select which tree you want to visualize, how you want to visualize it and will allow you to download the data.
a.- This will provide the list of trees where your protein of interest has been used as seed. There is the possibility that this list is empty. In this case the protein has never been used as seed.
b.- This option will allow you to switch evolutionary models that were used in the phylome. When building trees in during phylome reconstruction, up to seven evolutionary models are tested. Maximum likelihood trees for only a few (1 or 2) of them are reconstructed and shown in phylomeDB.
c.- We call collateral trees those trees in which the sequence of interest appears but has not been used as seed. This list of trees can be found here. If the sequence was never used as seed, the tree shown in the tree page will be a collateral tree.
d.- This row of tools will allow you to manipulate the tree image and download data. The first two tabs will open additional menus. The first one pertains to the annotations shown in the tree. Those annotations that are checked are currently shown in the tree image, such as pfam domains or the species name. If you want to show an additional feature, you can just mark it on the menu and click on Refresh. Not all leaves in the tree may have all the features, for instance genomes that were not taken from Ensembl will not have an ensembl annotation. The second menu is a search menu, it will allow you to search for leaves in the tree that fulfil a particular requirement such as species name or taxonomic group. The remaining tabs will allow you to download the data specific for the tree or to see the alignments.
The tree image can be modified using different commands that are encoded in menus shown when clicking on the internal nodes or leaves of the tree.
a.- The tree image in itself encodes several features that may be of interest for the user. By default the leaves will be shown by the code they were initially integrated into phylomeDB. Next to them the name of the species they belong to will be also displayed. The nodes are coloured depending on whether they are speciation (blue) or duplication (red) nodes. Also, for each tree, an aLRT support is calculated, if this support is lower than a given threshold the number will be shown and a bubble will can be seen around the node. The bigger the bubble, the more unstable the node is.
b.- Clicking on an itnernal node will show the menu found in b. This allows small manipulations in the tree such as swaping the order of the children in the tree or setting the root at this point. Information of the taxonomic age of the node can be also found here. This age is calculating by seeing which taxonomic group is the common ancestor of all the leaves derived from this node. The branch length and support are also displayed on the top of the menu.
c.- Clicking on a leave will give similar options for modifying the tree but will also offer additional information pertaining to the leaf itself. So, for instance, the complete lineage of the species can be found there as well as other annotations (uniprot or ensembl codes, internal phylomeDB code, etc...). The lower part of the menu will allow you to access the sequence page from phylomeDB as well as link to external databases such as UniProt, Ensembl, NCBI Taxonomy or metaPhOrs.
d and e.- Leaves can be marked with two kinds of bubbles: a green bubble can represent the protein that was used as seed to reconstruct this particular tree or the protein you were looking for. A yellow bubble marks the results of a search.
Next to the tree additional features can be marked. Right now there are two features implemented: Taxonomic range and protein domains.
a.- Taxonomic range: This marks in different colors the different taxonomic groups to which a species or group of species belong. A leaf can belong to different taxonomic ranges of different levels (order, sub-order, family...). This can give an idea on how well the tree conforms towards the NCBI taxonomic classification.
b.- Protein domains mapped according to Pfam can be found here. Each line represents the protein sequence where domains are represented in different shapes and colours while sequence regions without domain are colour-coded according to the amino-acids encoding the sequence. Straight lines represent gaps in the alignments.