What is new in phylomeDB 4?

News on the tree searching engine

The backend of the tree searching engine has been improved to provide a gene-centric view of all phylomeDB resources. Thus, after a protein or gene search, all the available trees in phylomeDB are listed and organized by phylome and tree type. Users can switch among all available seed and collateral trees without missing the focus on the searched protein or gene.

News on the visualization interface

In phylomeDB v4 all the information available for each tree is now shown using an integrated layout in which tree topology , taxonomy data, alignments and domain annotations, and event-age (phylostratigraphy) information are rendered in the same figure using the newest visualization features provided by the ETE toolkit v2.2:

i) PFAM domains, have been mapped to each alignment in our database and are now displayed in a compact panel at the right side of the tree (Figure 1e). For each sequence, domains and their names are shown, they can be clicked to obtain a short description and the external link to PFAM (Figure 1i). Protein regions not mapped to domains are shown using the standard amino acid color codes, while gap regions are represented by a flat line.

ii) A taxonomy-information panel has been added to the right side of every tree that allows to highlight the main taxonomic clades present within each gene tree. Information on the estimated the relative age (i.e. phylostratygraphy) of each tree node (18), as well as extended taxonomic and GO functional information, is provided through the contextual menu available by clicking.

iii) Tree images have been also simplified to improve readability. Mappings and/or cross-linking to general and organism-oriented databases has been extended to include the major Arabidopsis thaliana sequence database TAIR , Drosophila’s Flybase , as well as the Ascomycete-based genome database Genolevures. By default a single sequence identifier is shown on the tree, prioritizing those that are more suited for human interpretation, but this can be can be adjusted through the tree editing menu. A conversion table among PhylomeDB unique identifiers and other identifiers is provided in the download section.

iv) Speciation and duplication events are indicated using different node colors andbranch support values are now automatically highlighted for lowly supported partitions using a transparent red bubble inversely proportional to the branch bootstrap or aLRT value.

v) Internal tree searches can be performed for any of the annotated node attributes  while links to other databases are provided through the contextual menu of the tree browser that appear when clicking any node .

News on the tree action menu

Users can download relevant data, including the whole database, a specific phylome or, from the tree entry page, the relevant data corresponding to that tree. In this new release we have implemented the posibibility to download orthology predictions from a tree in the recently-developed OrthoXML standard format, in addition to a tabulated format.

News on the web-API

Finally, the web-based linking API has been improved and it now allows for direct links to trees and phylomes as well as highlighting custom nodes within a tree topology . The URL format used by the API is detailed in Table 1.