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Phylogenetic informativeness profiles for the OrthoMaM data set. (a) Chronogram and the calibration points used to calculate site rates. Phylogenetic informativeness profiles over a 190 Myr period for (b) four amino acid sequence alignments and (c) four DNA sequence alignments, on the same time scale as in panel (a). Integration of the area below the profiles can provide a ranking of the predicted utility of genes for that epoch (here, the epoch encompassing the branch leading to primates).  
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Normalized RF valuesare calculated by taking the plain RF value and dividing it by 2(n-3)where n is the number of tips in the phylogeny. Prior to calculatingan RF value, PhyKIT will first determine the number of shared tipsbetween the two input phylogenies and prune them to a common set oftips. Thus, users can input trees with different topologies andinfer an RF value among subtrees with shared tips. Provide a single column file with the names of the tipsin the input phylogeny you would like to prune from thetree. Requires a taxa file, which species which tip namesare expected to be monophyletic.  
When mixing codon and DNA data in a partitioned analysis, the branch lengths are interpreted as the number of nucleotide substitutions per nucleotide site! This is different from having only codon data, where branch lengths are the number of nucleotide substitutions per codon site (thus typically 3 times longer than under DNA models). This ensures users can quickly locate reliable information across a range of subjects on any one topic. A robust search functionality is an essential tool for efficiently navigating content landscapes. Users can input keywords or phrases to quickly locate specific information, making the discovery process more targeted and user-friendly.  
Furthermore, our analyses demonstrate that the original phylogenetic informativeness method can be extended to trees with more than four taxa. Thus, although the method currently predicts phylogenetic signal without specifically accounting for the misleading effects of stochastic noise, it is robust to the effects of homoplasy. The phylogenetic informativeness rankings obtained will allow other researchers to select advantageous genes for future studies within these clades, maximizing return on effort and investment. Genes identified might also yield efficient experimental designs for phylogenetic inference for many sister clades and outgroup taxa that are closely related to the diverse groups of organisms analyzed.  
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[Under certain modelsof molecular evolution, this type of site would be informative]. Portions of these phylogramsshown as '|' are branches, and '__' isthe internode. The most closely related pairs of taxa are on eitherside of the internode.