You need at least 256Mb of memory, and Java (v1.5+) to run TIQ. If it is not installed on your computer, please update Java or visit this page.
TIQ is a Java Web Sart application that allows browsing phylogenetic trees of toxins (from toxin-antitoxin systems) detected via the program TAQ v1.0 (Guglielmini, Szpirer & Milinkovitch, 2008).
Four toxin-antitoxin families were studied: RelE/ParE, MazF, Doc and VapC. For each one, three trees were built :
- One tree using the dfit supertree method implemented in the program Clann.
- One tree using the 'ancestral sequences method' described in Guglielmini, Szpirer & Milinkovitch, 2008.
- The Adams consensus (built in PAUP*) among the trees obtained using the two above-mentioned methods.
The CcdB family has also been investigated. But because of the low number of sequences we found, we just built a MrBayes tree.
TIQ has the following functionalities:
- Zooming in/out anywhere in the tree.
- Searching for sequences; just type a keyword (e.g. the name of a sequence, the name of an organism), or a GeneID (as provided on the NCBI web site) or paste the amino-acid sequence (or part thereof). The results, if any, are colored in orange.
Please discover the new features.
- Selecting (by clicking) one clade colors branches in purple.
- Selecting a sequence name prompts the display of the GenBank file information (as provided on the NCBI web site, database revision : September 2008) at the bottom of the window.
- Selecting sequences according to the taxonomy of their host. Just select a category in the upper-left menu. The results, if any, will be colored in purple.
- For the trees obtained by MrBayes, TIQ displays the clades posterior pobabilities (numbers at the nodes).
Here are the links to access trees (please, be patient while the tree is loading). When clicking on a link, a file will be downloaded on your computer. If it is not automatically executed, please do it manually (this will launch TIQ). The file will be erased when leaving the program.
- For the ParE family:
- For the MazF family:
- For the Doc family:
- For the VapC family:
- For the CcdB family: