Your query

Query taxa

Example

Enter a subtree or a list of comma-separated species to include:

Enter a subtree or a list of comma-separated species to exclude:

Check for monophyly.

Is the subtree monophyletic? Yes No

Specify taxa to ignore during tree search:

Results of your query

Go back to query

Taxa to include:

Taxa to exclude:

Search type:

Terms to ignore:

Click on a row to view the tree for that gene.

Name	Description	Number of taxa

Go back to query

Result for

Go back to results Tree Example

Please see the Help section for a full explanation on how to manipulate and navigate the tree. Briefly, ... [show] drag the mouse to move the tree, use the wheel to zoom, drag the mouse with the key down to rotate the tree (see "more options" in menu for sticking effect settings), use the wheel with the or key down to change respectively the height or width of the tree. Finally you can move the mouse over the nodes to see some informations about them or click the nodes to interact with them. [hide]

Help

Please note that the help for the database is not complete yet. It will be uploaded shortly.

Data stored

The database stores two types of data:

alignments for each DNA regions identified. We use the method of MacMahon and Sanderson (2007) to identify clusters of sequences. The alignments are then automatically generated using the software muscle. So far, there is no manual editing of the alignment and they are provided 'as is'. You are free to download the alignment and align it yourself. If you decide to do so, please keep us informed so we can upload better alignments!
phylogenetic trees for each DNA clusters. They are built using RAxML.

Type of queries

The database is phylogenetically oriented, which means that all queries start by inputing some species names or subtrees. Please follow the guidelines below to submit a query.

Creating your query

The first step is to enter the set of taxa you're interested in. This can be done as a comma-separated species list, or as a newick tree. Please look at the examples below for more information.
You have the possibility to search DNA regions available for these taxa (button 'Including') or do not contain these taxa (button 'Excluding').
If you entered a subtree in entry 1, you can request the taxa to be monophyletic (button 'Yes') or not (button 'No').
You can precise further your query by entering a list of comma-separated species you don't want to consider in the search.
Finally, just click submit.

Step 1 is the only required field, the steps 2 to 4 being set to default values if nothing is changed.

A successful query will result in a list of genes containing the taxa you specified. You can then visualize the alignment and the phylogenetic tree associated directly in your web browser (thanks to the Jalview applet!).

Examples

Here's a few examples to help you formulate your queries.

Example 1: Searching for a single species

Let's imagine you're interested in wheat evolution. You would like to know all the existing genes sequenced for the species Triticum aestivum and see their phylogenetic tree. You simply have to enter this to get the list of genes containing this species. Species names are stored as Genus_species (ie put an underscore between the two names).

You can also reverse the query and search for the genes that do not include this particular species. This is simply done by clicking the 'Excluding' button (Step 2).

You can also query on the genus name only (ie Triticum in the example). By doing so, you can ask the genus to be monophyletic or not.

Computational Phylogenetics