Download a test file

Welcome to the PhylteR application!

Here you can visualize and detect outliers in a list of gene trees.


First of all, you must add a tree file in Newick format.

Then, If you want to detect outliers, you should turn on the Detection button and then choose the parameters you want:

- nodal and patristic are methods to calculate distances between species.

- k is a threshold of the outlier detection. If k is big, the detection is more stringent.


You can then visualize your data by clicking on the several tabs!




contacts:

Aurore Comte - aurore.f.comte@gmail.com
Damien de Vienne - damien.de-vienne@univ-lyon1.fr
St├ęphane Dray - stephane.dray@univ-lyon1.fr




Projection of each tree on a compromise space (from Distatis method). The center of each cloud is the mean position of a species in the compromise. Each circle is the position of this species in a particular gene. The line between the center of the cloud and a circle is the distance between the reference position of the species and its true position in a particular gene.
Between genes space. Each circles represents genes. Genes with larger projections on the first axe are more similar to the other genes than genes with smaller projections.
Heatmap of the correlation matrix between genes
The 2WR matrix (two-way reference matrix) is a matrix genes x species computed by calculating, for every species, the distance separating its position in each gene tree to its mean position. The darker a pair gene/species is, the further it is from its reference position. You can zoom by brushing and doubleclicking on the plot
Grey circles are the mean of distance between species for a particular species. Red circles are genes. For a given gene, the distance between the species of interest and an other one is given by the shape of the red line: an acute angle mean an important distance between two species
For a given gene, eac withProgress(message = 'Making plot', value = 0, red line correspond to a species and each point on the red line correspond to the distance between this species and the other species. Grey circle is the mean distance between species for this given gene.