ATGC: PhySIC

PhySIC_IST: cleaning source trees to infer more informative supertrees.

Scornavacca C., Berry V., Lefort V., Douzery E.J.P., Ranwez V.
BMC Bioinformatics. 2008, Oct 4;9:413.

Please cite THIS paper if you use PhySIC_IST.

PhySIC_IST online execution

User guide

More explanations are given in this document .

The online interface

It is a web form that you fill with your data and values for the program options, your name; 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

Source tree file
The input source tree file contains source trees encoded in standard Newick format, possibly containing edge lengths and bootstrap values.
Below is an example of the Newick format for a tree containing bootstrap values and edge lengths:
Backbone tree (optional)
You have the possibility to input a starting backbone tree in which missing taxa of the source trees are inserted. This file contains the backbone tree you proposed. This backbone tree is possibly simplified if not satisfying the PC property.
Outgroups for tree rooting (optional)
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 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.
Below is an example of the format suitable for outgroup_File:
```
Monodelphis
Echinops, Loxodonta, Dasypus
     
```
Using the specified outgroup levels, the unrooted tree:

will become:

The unrooted tree:

is discarded from the analysis because none of the outgroups taxa are present in the tree.

The unrooted tree:

is discarded from the analysis because the outgroup (Dasypus, Echinops) is not monophyletic.
Bootstrap threshold for source clade selection
Before computing the supertree, the program first collapses source tree branches having a bootstrap proportion (bp) lower than the indicated threshold. Hence, only significantly supported clades are considered for supertree building (this is especially important with veto supertree methods). For instance, if bps range from 1 to 100 in the source trees (as in the above example), you can typically use 70 as a clade selection threshold.
Source trees that do not contain bp are not affected by this collapsing step. Thus, the input file can contain a mix of trees with bps and trees without. Note that trees with only some bp missing, are not considered by the collapsing step. If you do not want the program to collapse branches at all, just set the treshold value to 0.
Correction threshold for anomalies detection
The correction threshold is the threshold used by the STC (Source Tree Correction) preprocess, aiming to detect anomalies in the source trees (e.g., resulting from paralogy, HGT events or long branch attraction).
The STC preprocess detects incongruences in the source trees on the basis of triplets of taxa present in the source trees. When conflicting resolutions are observed among source trees for the same three taxa, STC drops the resolutions that are statistically less supported. This is achieved by a Chi-Square test comparing the frequencies with which the conflicting resolutions respectively appear. The correction threshold is a real value between 0 and 1. The higher it is, the larger the difference between frequencies of conflicting resolutions has to be in order for STC to drop the least frequent alternatives. In other words, setting the correction threshold to 1 impedes STC to drop any input triplet, hence leaves the source trees as they are, while setting it to 0 implies removing from the source trees any contradicted triplet (e.g. ab|c) that is globally less frequent that an alternative resolution (e.g. ac|b). In the former case, PhySIC_IST behaves as a pure veto method, while in the latter case it mimics a voting (i.e., liberal) supertree method.
When STC drops some triplets, the source trees are modified in order that those triplets are not displayed anymore.

Results

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

The supertree inferred by PhySIC_IST is outputted in Newick format. It can be visualized with usual tree viewing/editing softwares such as TreeDyn, Treeview X or DendroScope.
PhySIC_IST also outputs the list of input taxa not inserted in the supertree (if any) and the value of the CIC for the proposed supertree. The CIC value measures the informativeness of the supertree (see the paper for details).
PhySIC_IST also outputs a "newForest" file. This file will contain the modified source trees.

Source tree file	File Example file

Backbone tree file (optional)

Outgroup file (optional)

Bootstrap threshold for source clade selection
Correction threshold used by STC (a real value between 0 and 1, with 0 asking to remove any triplet as soon as it is less frequent than an alternative triplet, while 1 leaves source trees unchanged)