Evolutionary biologists now have to deal to an increasing extent with many phylogenetic trees and user-friendly bioinformatic tools are needed for handling large tree collections. Such tools are especially relevant for tasks that are cumbersome to perform manually, such as validating taxon names using a reference taxonomy, providing taxon sampling statistics, or pruning source trees so that they only contain taxa from a taxonomic group of interest. Such questions are crucial in phylogenomics, where phylogenies are mainly obtained by concatenating gene sequences into large molecular datasets (e.g. supermatrix approach) or by combining individual trees inferred separately on each gene (e.g. supertree approach). Several problems addressed here from a tree framework standpoint only take their constitutive taxa into account. Described solutions are thus also suitable for many other kinds of data (e.g. sequence alignments, morphological measures), for which taxonomic representation is essential.

Knowing how many different taxa belonging to a particular taxonomic group (e.g. placentals) are represented in a tree collection, determining how many trees contain at least one placental, finding these trees, and pruning them from every taxon except mammals are various tasks that cannot be performed without mapping user taxa to a reference taxonomy. It is relatively complicated to compute such a mapping 1, but the results can enable powerful tree search, while also providing pruning functions and relevant statistics.

In order to manage tree collections, taxon names first have to be identified and then placed in a reference taxonomic scheme. PhyloExplorer allows the user to choose between two such schemes: the NCBI Taxonomy 9 and the Catalogue of Life 2008 Annual Checklist 10 from the Integrated Taxonomic Information System (ITIS) 11. Most published phylogenies use a liberal naming scheme that combines taxonomic information with other kinds of information such as gene names, sequence identifiers or geographical origins. For example, when a tree inferred using the BRCA1 gene contains a domestic mouse among its taxa, its label can be either: mouse, BRCA1_mouse, Musmusculus_NM_015745, and so on. This freedom may allow the user to uncover some relevant information, but it also impedes simple automatic determination of the taxon represented by the given name. We use a naming convention to facilitate this determination without any loss of generality. The principle is to use separator characters chosen by the user to distinguish among the various pieces of information encompassed in the taxon name. The complete name is thus split into several words, with the first ones being used to identify this taxon within the reference taxonomy while others can be used freely for storing any other kind of information. We adopted this naming convention because it is so frequently used in TreeBASE that it almost seems to be a de facto standard. Most taxonomic terms consist of a single word (e.g. higher-level taxa), but some consist of two distinct terms to reflect the Linnean "genus-species" classification or to avoid ambiguity. Indeed, the reference taxonomy may contain ambiguous names because of name homonymy and synonymy. For example, Echinops is both a plant genus and a mammal genus. In this case, two distinct taxa have the same genus name and additional information can be provided between "<" and ">" to overcome this ambiguity. In the NCBI taxonomy, Echinops is annotated as either "Echinops < mammal >" or "Echinops < plant >". When a taxon name is composed of several words, PhyloExplorer first checks if the whole name corresponds to a term of the reference taxonomy. If the check fails, the last word is ignored and the thus-obtained shorter name is checked against the taxonomy – this shortening operation is repeated until the name is found within the taxonomy or is reduced to an empty string. For example, the following names respect our naming convention: mus, mus_BRCA1, mus_musculus_BRCA1_France, echinops_<mammal>_BRCA1, when using the underscore character as a separator.

PhyloExplorer also proposes a function that allows users to perform taxonomic queries on trees stored in TreeBASE 2. For this purpose, the content of TreeBASE was obtained from its ftp server ftp://www.treebase.org/pub/treebase. The 3,696 studies available as of September 2008, containing a total of 6,237 trees and 93,013 taxa, were collected. Since the trees available in TreeBASE have been provided by different scientists without adopting a common naming convention, a considerable proportion of the taxon names are not scientific names present in the reference taxonomies. For TreeBASE taxon names not present in the NCBI taxonomy (i.e. less than 33%), we relied on the TBMap tables which translate most TreeBASE taxa into proper scientific names based on a number of taxonomic databases (IPNI, uBio, ITIS, RDMP) 3. This allowed identification of a further 8% of the taxon names.

PhyloExplorer is written in the Python language and has been implemented according to the Django web framework 12. Django is a stable and powerful system that is able to handle thousands of page views per second and to associate a graphical user interface with complex manipulations of an underlying database. In our case, the database is composed of relational tables encoding NCBI and ITIS taxonomies and a version of TreeBASE curated as detailed above. The database is handled by the MySQL database management system 13. Although a Django project can consist of several applications, PhyloExplorer has currently only one application called "DjangoPhyloCore". "PhyloCore" is a wrapper of this library that enables users to access it outside any Django project, i.e. to use its facilities under the Python interpreter as if it were a standard library.

The UML diagram structure of the "PhyloCore" library (Fig. 1) is composed of several classes. Most of them allow interaction with the corresponding tables in the database since Django imposes a class for each table of the database. The class "Tree" is used to store phylogenies as individual objects, including the Newick format and other associated properties such as a name or the tree's rooting status.

"TreeCollection" is the main class of the project and allows storage of user tree collections, TreeBASE itself, and sets of trees extracted from TreeBASE through the querying system. The queries are performed through functions of this class. The "TreeCollection" class also provides functions to filter trees by pruning them (e.g. restricting them to a taxonomic group of interest) and to obtain statistics on taxon coverage among trees. The "Taxonomy" class references all taxa of the current reference taxonomy (NCBI or ITIS) as well as their synonyms, homonyms, and hierarchical relationships between higher-level taxa. The "Rank" class encodes the taxonomic rank of the taxa (kingdom, phylum, class, family, genus, species), exactly as in the ITIS database 11. The "TaxonomyReference" class provides useful functions common to trees and tree collection querying facilities. Lastly, the "BadTaxa" class stores taxa from currently managed tree collections that are not found in the chosen reference taxonomy.

The "PhyloCore" facilities can be accessed through a graphical interface provided by the PhyloExplorer web server. This server allows several users to simultaneously query "PhyloCore" and its database. The web server was developed using the CherryPy object-oriented HTTP framework for Python 14. The NetworkX Python package 15 enables implementation of the browsable tree structures. PhyloExplorer relies on the PHY.FI graphical tool 16 for displaying labeled trees and also links to the PhyloWidget applet 17 for a less static tree display. Taxon pictures are extracted from the corresponding Wikispecies 18 and Wikipedia 19 pages. The PhyloExplorer source code is distributed under the CeCILL license version 3 20, a French variant of the GNU GPL licence adopted by the Centre National de la Recherche Scientifique (CNRS). It can be downloaded from the following Google Code project page: http://code.google.com/p/taxomanie/.

Many software packages propose to display and handle single user trees or collections of trees such as the long-standing classic Treeview 21, the sophisticated TreeDyn 22 and the rising star Dendroscope 23, among others. Websites aiming at interactively displaying phylogenetic trees, such as PHY.FI 16, iTOL 24 and PhyloWidget 17, for example, have also recently flourished. However, most of these tools are tree rendering programs that only allow the user to graphically manage trees and associated annotations in some cases. Database orientated web servers such as TreeFam 6 and PhyloFinder 25 permit taxonomic querying and retrieval of phylogenetic trees from dedicated databases. Whereas others, like GRUNT 26 and Summary Tree Explorer 27, implement some tree filtering and pruning features according to the taxonomy. However, none of these latter tools can be used to upload and explore user phylogenies or obtain detailed summary statistics on user tree collections. The only programs providing basic statistics on data availability are Clann 28 for tree collections in the context of supertree reconstruction, and PhyloTA Browser 29 for molecular datasets. In fact, PhyloFinder 25 is the closest conceptually to the PhyloExplorer tool presented here, but it is currently restricted to trees stored in TreeBASE and does not allow obtaining taxonomic coverage statistics or performing complex taxonomic queries.

A typical use of PhyloExplorer begins by uploading a tree collection on the website in Newick or Nexus format. A simple taxon list can also be entered as a trivial multifurcated tree. This allows users to deal with various kind of data (e.g. sequence alignments, morphological measures), for which the taxonomic representation is important. The trees are then parsed and taxon labels are mapped against scientific names from the chosen reference taxonomy (either NCBI or ITIS) with listed homonyms and synonyms. For automatic correction, the user is provided with a list of alternatives for up to ten unrecognized names. The corresponding excerpt of the reference taxonomy, including only mapped taxa, is then displayed. Two statistics are provided at each taxonomic rank. The first states the number of user trees containing a representative of the corresponding taxonomic group. The second states the number of representatives of this taxonomic group encountered in the user tree collection. Each mapped taxon is provided with a link to the corresponding entry in the NCBI or ITIS database. For pedagogical purposes, available pictures from Wikispecies 18 or Wikipedia 19 are popped up when browsing the taxonomic excerpt. Links to the corresponding iSpecies 30 and Wikispecies 18 pages are also provided for each taxon. A taxa × trees matrix scoring the presence or absence of taxa in trees of the user collection can be generated to visualize the taxonomic overlap among trees. The user can then perform several operations on the input collection, such as: browsing the taxonomy excerpt corresponding to each input tree; restricting its trees to a subset of species by a simple mouse click; mining a relevant subset of trees through a simple querying language; and locating trees in TreeBASE matching taxa of the input collection.

When PhyloExplorer is provided with a tree collection, either by simple upload or by searching TreeBASE, every leaf label is mapped to terms contained in the reference taxonomy. These terms include scientific and common names with their official taxonomic synonyms and homonyms. The lack of a single universal reference taxonomy 1 led us to consider several existing alternatives. By relying on the comprehensive, widely used, and up to date NCBI and ITIS taxonomic projects, we hope to be able to fulfil a broad spectrum of evolutionary biologists' needs. The PhyloExplorer taxon naming facility helps to detect misspelled or taxonomically incorrect taxon names and proposes corrections according to known synonymies. Leaf labels that cannot be mapped to the reference taxonomy are listed, as well as those having an ambiguous taxonomic name. As automatic correction is error prone, the user is prompted to correct problematic taxon names by selecting the appropriate name among close alternatives present in the reference taxonomy. Then PhyloExplorer will automatically correct taxon names accordingly in the whole tree collection. Corrected trees can be downloaded afterwards, as well as the detailed list of corrections.

For example, we checked the 77-taxa metazoan phylogenetic tree from the recent study of Dunn et al. 31 (Fig. 2, Additional file 1). Using the NCBI reference taxonomy resulted in successful mapping of 76 leaf labels, including one homonym and three synonyms (Fig. 3A). Only one label (mertensiid_sp) could not be found in the reference taxonomy because it represents an English common name for an unidentified member of the family Mertensiidae. PhyloExplorer correctly suggested this name correction (Fig. 3A). By contrast, when using ITIS as the reference taxonomy, only one synonym and 13 labels that could not be mapped were revealed (Fig. 3B). This illustrates the differences in name mapping resulting from different taxonomic schemes. We hope that semi-automating this fastidious, but nevertheless essential task will encourage researchers to check the validity of their trees before depositing them in phylogenetic tree databases such as TreeBASE. This tree proofing stage is much easier with PhyloExplorer than with any other existing tool.

As an illustration, we considered the collection of 146 individual gene trees from the phylogenomic study of Delsuc et al. 32(Additional file 2). This example is of particular interest because its trees contain both binomial species names and higher taxonomic rank names. The latter labels designate chimerical taxa assembled from gene sequences of different representatives, as is often the case in supermatrix studies 33. Once this collection has been uploaded, PhyloExplorer produces simple statistics to depict it within the "Statistics & queries" view. Both tree size and taxon frequency distributions are summarized through graphical plots (Fig. 3A). The general information states that this dataset consists of a total of 146 trees containing 38 distinct taxa. The tree size distribution indicates that the smallest tree contains 18 taxa. The taxon frequency distribution reflects the substantial overlap among these trees, with no taxon appearing in less than 42 trees among 146 and most taxa occurring in more than a hundred different trees. When selecting the "Matrix trees × taxa" view, a data availability matrix is constructed from the collection (Fig. 3B). This representation provides a general overview of the degree of overlap among trees from the collection in the form of a matrix scoring the presence (blue squares) or absence (white squares) of each taxon in each tree. This matrix can easily be browsed by pointing the mouse on each matrix cell to display its associated taxon and tree name information. The detailed data availability matrix can also be downloaded in csv format (compatible with most spreadsheet programs) for use as supplementary material in supertree and supermatrix studies, for example.

By coming back to the "Statistics & queries" view, a summary excerpt of the reference taxonomy containing all mapped taxa is provided as an interactive tree (Fig. 3C). For educational purposes and to facilitate browsing of the taxonomy, images from Wikispecies 18 or Wikipedia 19 are automatically popped up when passing the mouse pointer over each taxonomic rank and taxon. The summary excerpt indicates, for each taxonomic rank, the number of its representatives contained in the tree collection and the number of user trees in which members of this taxon are represented. Based on these indications, it can easily be seen that four different cnidarians are represented in the whole tree collection and that 146 trees contain at least one cnidarian. A simple click on the first number allows the user to prune trees so that they only contain cnidarians, while clicking on the second will restrict the collection to the subset of trees containing at least one cnidarian. This latter function allows the user to easily restricting the tree collection to subsets of trees containing members of a particular taxonomic group or a terminal taxon of interest. PhyloExplorer also enables more complex and flexible tree restrictions by selecting relevant taxa through the corresponding checkboxes. Once the internal nodes of interest are selected, PhyloExplorer restricts the trees of the current collection to these taxa (Fig. 3D). The summary statistics are updated accordingly, and the modified collection can then be browsed through the taxonomic excerpt and downloaded in Newick format.

The "Individual trees" view offers the option of browsing trees from the collection individually. A list of all individual trees is given with links for displaying each tree using the PhyloWidget 17 applet (Fig. 4A). Provided that trees have been named in the Nexus formatted collection, individual trees are listed after this name. Once a particular tree is selected, i.e. the tree from the if2p gene in the current example, its internal nodes are automatically labelled by PhyloExplorer with taxonomic ranks when they can be unambiguously inferred. The resulting decorated tree is rendered using PHY.FI 16 within the "Image" tab. The "Browsable taxonomy excerpt" tab allows the user to browse the tree in the reference taxonomy context with taxon image pop-ups and links to the iSpecies 30 and Wikispecies 18 pages of each taxon (Fig. 4B). Finally, the "Newick format" tab provides access to the labelled tree in Newick format (Fig. 4C).

Finding a particular phylogeny in phylogenetic tree databases, or more generally in tree collections, is often like trying to find a needle in a haystack. Indeed, though confronted with phylogenetic tree databases containing thousands of trees, the user is usually offered only basic query capabilities. Recent efforts have been made in the right direction in the particular case of TreeBASE with tools designed to taxonomically validate the trees (TBMap) 3 and provide enhanced query options (PhyloFinder) 25. However, a general system allowing complex taxonomic queries to be performed on taxonomically validated tree collections is still lacking. PhyloExplorer now offers this possibility.

For instance, we extracted a tree collection from the OrthoMam database 7 by performing a request aimed at selecting trees inferred from slow evolving markers (rate ≤ 0.5) of reasonable size (length > 1000 nucleotide sites). This led to a collection of 79 trees which was uploaded into PhyloExplorer (Fig. 5A, Additional file 3). This tree collection contains a total of 25 mammalian taxa for which complete genome sequences are available in the EnsEMBL database 8. A question of primary interest in mammalian phylogenetics is the order in which diversification among the four major placental groups (Afrotheria, Xenarthra, Euarchontoglires and Laurasiatheria) occurred – a problem that is directly dependent upon the position of the placental root 34. When studying the position of the root of the placental tree, it is better to consider trees or molecular datasets containing at least six eutherians and one representative of each major placental clade, plus a marsupial or monotreme outgroup. Such trees can be located very easily in PhyloExplorer by applying the following query to the OrthoMam trees under the "Search trees" tab: {EUARCHONTOGLIRES}>0 and {LAURASIATHERIA}>0 and {AFROTHERIA}>0 and {XENARTHRA}>0 and ({METATHERIA}>0 or {MONOTREMATA}>0) and {EUTHERIA} > 6. For each tree T of the current collection, PhyloExplorer replaces {TAXONOMIC_GROUP} by the number of representatives of this taxonomic group within T. Tree T matches the query if the resulting Boolean expression is true. The above query returned 23 candidate trees, while providing an even sampling of the major placental clades (Fig. 5B). Then, the user can conduct a supertree analysis from the indicated subcollection with an external tool. Alternatively, the user can collect the corresponding datasets in the OrthoMam database to construct a supermatrix with an optimal distribution of missing data with regards to the biological question at issue.

PhyloExplorer's query language can also be used to mine trees from the TBMap-curated version of TreeBASE. The same request for mammalian trees on TreeBASE results in 13 trees containing a total of 210 distinct taxa from which a supertree can be reconstructed. This querying of TreeBASE is also helpful for supermatrix studies, as primary data matrices can be downloaded from the TreeBASE website once relevant study numbers have been identified thanks to PhyloExplorer. Finally, the "Pruning trees" tab provides an easy way to restrict tree collections by defining taxonomic filters. Once filters have been defined, trees can then be restricted to include only taxa respecting these filters, or alternatively be pruned from the taxa defined in these filters. This function can be particularly useful for testing the influence of taxon sampling on diversification studies which require handling and statistical analysis of very large trees 35.

The TBMap-curated version of TreeBASE 2 we use includes 6,237 trees. However, its taxonomic coverage is highly irregular, with some groups being much more represented than others. Moreover, islands of taxa exist in which constitutive taxa are not linked by any tree to other taxa. This has, in particular, been pointed out by Page 3, who provided several graphical views of the situation as of 2004. However, a more detailed and live picture can be obtained as TreeBASE is available as a specific collection in PhyloExplorer. The complete TreeBASE tree collection can be queried taxonomically from the PhyloExplorer front page (Fig. 6A). This enables the user to query and investigate its taxonomic coverage much more closely and dynamically than is possible when using the TreeBASE website interface or even the PhyloFinder dedicated tool 25. Note, however, that some taxa appearing in TreeBASE cannot be mapped to our reference taxonomies despite the use of the TBMap-curated version of TreeBASE 3. Also, the query result depends on the chosen reference taxonomy. For example, the simple query {mammalian}>0, allows retrieving all trees from TreeBASE that contain at least one mammal (Fig. 6A). Using the NCBI reference taxonomy results in 553 trees containing 5,371 different labels of which 5,075 (including 23 homonyms 176 synonyms) are successfully mapped to 3,660 distinct taxa (Fig. 6B). Whereas, using the ITIS reference taxonomy returns 566 trees containing 6,404 different labels of which 5,054 (including 10 homonyms, 127 synonyms and 1 vernacular) are successfully mapped to 3,677 distinct taxa (Fig. 6C). We plan to annually update the TreeBASE content of our site.

PhyloExplorer also provides a useful educational tool for assessing a taxonomic group that the user is not familiar with. This feature could be of particular value when preparing practical courses for undergraduates. Indeed, when uploading a tree or a list of taxa of interest, PhyloExplorer constructs an excerpted version of the corresponding taxonomic tree that can be browsed interactively. Internal nodes of the taxonomic excerpt tree are labelled by the name of the smallest taxonomic rank containing all taxa belonging to this group. For example, PhyloExplorer can be used to quickly view and browse the taxonomy of taxa represented in the NCBI Trace Archives 36. Pictures of taxa available in Wikispecies 18 can be popped-up by positioning the mouse pointer over the corresponding taxon name. Clicking on taxon names will redirect the user to the full taxon description in the NCBI Taxonomy Browser 37, which indicates the number of nucleotide sequences available for that particular taxon. PhyloExplorer also provides a link to automatically perform a search for each taxon in the iSpecies engine 30, which returns information on the geographic distribution, available pictures on the web, and associated bibliography. A link is also given for each taxon to the corresponding Wikispecies page for additional information.

Taxon pictures are of great educational value in many cases in which a phylogeny is to be shown or described. It is indeed common practice to display such taxon images at the tips of phylogenies in slide presentations, posters, and publications. Such pictures can be found on dedicated websites such as Wikispecies or Animal Diversity Web 38, or through search engines such as iSpecies. However, manually typing each taxon name in these websites can be cumbersome and is prone to spelling errors. PhyloExplorer automates this task by providing a feature to get available pictures from Wikispecies for all terminal taxa of an input tree or tree collection and for all taxa of a taxon list. Shifting to the "Taxon images" view prompts PhyloExplorer to display, by default, available images for the first 20 taxa. Annotated thumbnails of retrieved images are returned and the collection of full-size images can be viewed as a slide show (Fig. 7). A link is also provided to launch the search for all taxon images in a separate window of the browser. The pictures can then be downloaded for direct use in scientific presentations and lectures. An interactive tree viewer program like Dendroscope 23 can also directly upload these pictures for display at the tips of trees by mapping taxon names with image filenames.