NOTICE: The PhyDesign website (not algorithm) recently underwent updates (11/01/2022) to fix user issues. If you encounter a bug, please contact us

To estimate phylogenetic informativeness profiles (Townsend 2007) , the PhyDesign web application is partitioned into of 3 components:

• a form to upload information and choose an application to calculate the substitution rates for each alignment site,
• a table listing the rate vectors produced by the analysis, including links for download, and
• a user-friendly graphical interface to plot phylogenetic profiles and calculate integration values.

To obtain the site rate distributions for each locus, we require for input (1) an alignment in Nexus or Phylip format of markers pruned to contain sequences only from taxa for which the tree topology is fairly well known, and (2) an ultrametric tree in Newick (recommended) or nexus format for those taxa. The ultrametric tree can be introduced as a chronogram (ultrametric tree with branch lengths proportional to time); if so, profiles will be aligned with respect to time.

1. Alignment: NONE UPLOADED
2. Tree: NONE UPLOADED

A link with the rate calculation results will be sent to the email address supplied below:

Alternatively, if you already know the rate distribution for each marker in your alignment you can input these rates and obtain the phylogenetic informativeness profiles directly. The file format to input the rates can be found here; in addition, a site rate file with the proper formatting will be generated after analyzing your alignments with the corresponding ultrametric tree by using the form above.

1. Vector file: NONE UPLOADED
2. Tree file (optional): NONE UPLOADED