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

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.



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.