WAVES '0.1.0Beta' version, mind this is beta!

Physic_IST - v1.0

Online since 20 Jun 2016, 12:38 p.m. / last update 12 Sep 2016, 3:48 p.m.

The source trees have to be contained in a text file (e.g., named "sourceTreeFile") with trees written in the Newick format.

The user has the possibility to input a starting backbone tree in which missing taxa of the source trees are inserted. The file myTreeFile contains the backbone tree proposed by the user. This backbone tree is possibly simplified if not satisfying the PC property.

newForestFile is the name of the file where the method outputs the modified source trees. This option is relevant only with -b and -c options.

When PhySIC_IST is provided with unrooted source trees, it first has to root them. To that purpose, the software incorporates a rooting tool that automates the procedure. This tool accepts as input different outgroup levels, specified in the file named outgroup_File. Each level is a list of comma-separated taxa. Each level of outgroup must be divided from the next one by a line break. The rooting procedure considers each unrooted source tree separately. For a given source tree T, it determines the first level of outgroup that contains one or more taxa of T. Then the tree is rooted on the branch leading to the smallest subtree hosting all outgroup taxa of this level present in the tree. In other words, unrooted source trees are rooted on the branch leading to the outgroup that is the farthest from the ingroup. If the proposed outgroup is not monophyletic, the tree T is discarded from the analysis. This procedure does not alter the resolution inside the ingroup nor in the different outgroup levels that can be present in the tree.

This is the file which contains the PhySIC_IST supertree