Phylogenetic trees are pervasively used to depict evolutionary relationships. Increasingly, researchers need to visualize large trees and compare multiple large trees inferred for the same set of taxa (reflecting uncertainty in the tree inference or genuine discordance among the loci analysed). Existing tree visualisation tools are however not well suited to these tasks. In particular, side-by-side comparison of trees can prove challenging beyond a few dozen taxa.
Allows users to draw and compare rooted phylogenetic networks. Dendroscope is a program that includes characteristics allowing researchers to treat realistic phylogenetic trees. It also provides an interactive platform for researchers to explore the application of rooted phylogenetic networks to their phylogenetic trees and data. Moreover, this tool is available with a graphical user interface (GUI) or a command line interface (CLI).
Enables the comparison of tree topologies, even in the presence of duplication and loss events. To do so treeKO recursively splits gene trees into pruned trees containing only orthologs to subsequently compute a distance based on the combined analyses of all pruned tree comparisons. In addition, treeKO implements the possibility of computing phylome support values, and reconciliation-based measures such as the number of inferred duplication and loss events.
Computs the quartet distance between two unrooted trees, i.e. the number of quartet topology differences between the trees, where a quartet topology is the topological subtree induced by four species. The QDist program is based on an algorithm with running time O(n log2 n), which makes it practical to compare large trees. QDist outputs the quartet distance in a format determined by the user.
An algorithm and software tool for comparing alternative phylogenetic trees. The main application of the software is to compare phylogenies obtained using different phylogenetic methods for some fixed set of species or obtained using different gene sequences from those species. The algorithm pairs up each branch in one phylogeny with a matching branch in the second phylogeny and finds the optimum 1-to-1 map between branches in the two trees in terms of a topological score.
Evaluates similarities and differences between phylogenetic trees. TOPD/FMTS combine two different programs to calculate this distance: TOPD and FMTS. First compares two trees with the same taxa or two pruned trees, and the second converts multi-gene family trees to single-gene trees. Both program have easy-to-modify parameters.
A web application to visualise and compare phylogenetic trees side-by-side. Its distinctive features are: highlighting of similarities and differences between two trees, automatic identification of the best matching rooting and leaf order, scalability to very large trees, high usability, multiplatform support via standard HTML5 implementation, and possibility to store and share visualisations. Phylo.io can easily be embedded in other web servers.
Deduces edit paths which commands evolutionarily reasonable constraints on the search space of edits. EEEP aims to decrease the overall computational burden while retaining the ability to build accurate solution sets. It was employed for inference of pathways of lateral genetic transfer (LGT) by comparing a set of 22 432 protein test trees derived from a microbial data set to a reference supertree.
Allows the exploration of change in hierarchically organized numerical data. TreeVersity is an interactive data visualization tool that focuses on the direction of change, real and relative change, start and end values, created and deleted nodes, and internal node values. This application includes a reporting tool, that guides users through the significant differences in the tree.
Analyzes a large number of simulated and biological datasets. BeeTLe is a simple heuristic that runs a collection of methods, including POY, a method which seeks a tree/alignment pair minimizing the total treelength. It produces a set of trees on a given input set of unaligned sequences, uses POY to compute the treelength of each tree, and then returns the tree that had the shortest treelength. It is guaranteed to find trees at least as short as those found using POY, and thus enables to evaluate the impact of using treelength to find trees.
Computes the similarity of two trees based on the number of shared four-taxon subtrees. SlowQuartet measures the topological information common to two trees. It provides a perspective on the relative merits of Bayesian and parsimony approaches to morphological phylogenetics. The method can be adapted in various ways to address pairs of trees that contain polytomies.
Compares a set of input trees. SplitDist was developed to (i) calculate the number of splits shared or differing between pairs of trees, (ii) calculate the union and intersection of splits in a set of trees, (iii) calculate the frequency the splits appear with in the set of trees, and (iv) annotate the trees’ edges with the frequencies to show the degree to which the individual edges are supported by the total set of edges.
Allows evaluation of the confidence of phylogenetic tree selection. CONSEL provides features to read the matrix of the site-wise log-likelihoods of the candidate trees. It can be applied to parsimony, the minimum evolution, or the least squares. This tool reads the bootstrap replicates of the log-likelihoods generated in amount. It can produce several p-values for the candidate trees; the Bootstrap Probability (BP), the Kishino-Hasegawa (KH) test, the Shimodaira-Hasegawa (SH) test, the Weighted Shimodaira-Hasegawa (WSH) test, and the Approximately Unbiased (AU) test.
A method for comparing unrooted phylogenetic trees with the Matching Cluster distance version. In addition, TreeCmp is implemented with other popular metrics for trees that can be computed in polynomial time (Robinson-Foulds (RF), Path Difference (PD), Nodal Splitted (NS), Triple (TT) and Quartet (QT)). All metrics implemented in TreeCmp take into account only the topology of compared trees, branch lengths are ignored.