PhySIC: a veto supertree method with desirable properties.

Ranwez V., Berry V., Criscuolo A., Fabre P.H., Guillemot S., Scornavacca C., Douzery E.J.P.
Systematic Biology. 2007 56(5):798-817.

Please cite THIS paper if you use PhySIC.

A new version of PhySIC is available here: PhySIC_IST

PhySIC online execution

A maintenance operation on the server hardware is scheduled on Wednesday August 24 at 14:00 (GMT+2).
The running jobs will be lost.
We apologize for the inconvenience.
Source tree file File Example file
 
Starting Supertree (optional)
 
Bootstrap threshold for source clade selection

Name of your analysis
Your email
Please confirm your email


User guide


The online interface

It is a web form that you fill with your data and values for the program options, your name and the country where you are; then click on the "Execute & email results" button to start the program with your settings; after a while you will receive your results by email.

For a quick start, simply select the "Example" radio button, type your email, and click the "Execute & email results" button. This will run the program with default values; the example tree file contains three trees in Newick format.

Options


Results

With the above input file you will obtain the following supertree in setting the clade threshold to 60:
PhySIC supertree

The outputted supertree contains labels (either PI, PC or PIPC) indicating the reason for each multifurcating node. These labels can be seen with usual tree viewing/editing softwares such as TreeDyn, Treeview X or DendroScope.
Mainly, PI indicates unsufficient overlap between the source trees to choose any possible resolution of the node; PC indicates that any further resolution of the node would contradict at least one source tree; PIPC is a combination of both phenomena, ie resolving further the node would result in either arbitrary branches or branches contradicting some soure tree(s) (see the paper for details).
To obtain a supertree as resolved as possible (under the constraints of the algorithm), as a rule, if you obtain mainly PC labels, try to increase the threshold, and if you obtain mainly PI labels, try to decrease the threshold.