Computes patristic distances from large trees. PATRISTIC generates scatter plots from ordered pairs of distances and calculates correlation coefficients and other statistics from distance matrices. It includes features for recognizing distance matrices calculated by other programs from other components of sequence data, such as evolutionary distances calculated from pairwise sequence comparisons.
Allows users to compress phylogenetic tree streams. tree-compression offers two mains features: (i) a simple compression able to parse a single that compresses its topology and branch lengths; (ii) and a Robinson-Foulds (RF) distance compression, able to handle two trees, which stores and compresses edit operations between those. The application also includes a function to decompress the files.
Allows exploration of the culture-gene co-evolutionary dynamics. This approach consists of an agent-based evolutionary simulation that extends an analytic and computational model. This model captures the Cultural Brain Hypothesis which relies on the idea that brains expand to store and manage more information. It provides a potential evolutionary mechanism that can explain a variety of empirical patterns involving relationships between brain size, group size, innovation, social learning, mating structures, and developmental trajectory, as well as brain evolution differences among species.
Permits investigation of recombination scenarios based on the bootscan principle along alignments of viral genomes. RecDetec is able to analyze alignments of genomes and phylogenetic information content. Furthermore, it enables researchers to display traces of recombination applying maximum likelihood phylogenetics.