DupLoCut computes ancestral gene orders, given a phylogenetic tree and gene orders assigned to the leaves of the tree. It attempts to find the most parsimony assignment of gene orders under the duplication-loss evolutionary model.
Phylonium is a program for estimating the evolutionary distances between closely related genomes. It is much faster than alignment based approaches for phylogeny reconstruction and usually more accurate than competing alignment-free methods.
Bosque is a distributed software environment oriented to manage the computational resources involved in typical phylogenetic analyses. Bosque has been implemented as a client-server application where the server can execute installed phylogenetic programs (Phylip, PhyML, TreePuzzle, Muscle) and the client manages the results on a local relational database, although it can also execute phylogenetic programs locally, useful when no server is available. The client also performs the graphical visualisation and edition of trees and alignments, providing an environment for the analyses, from the integration of sequences to the printing of a final tree.
bdvis provides a set of functions to create basic visualizations to quickly preview different aspects of biodiversity information such as inventory completeness, extent of coverage (taxonomic, temporal and geographic), gaps and biases.
MetaTreeMap (MTM) is a module developed to visualize phylogenic trees where each species (node) has a number of reads (quantity) that map on the reference genome of this species. Each species is represented by a rectangle and its area is proportional to the number of assigned reads. The final figure is nested rectangles representing tree branches.