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).
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.
Produces multiple alignments and trees from genomic data. Hal is a phylogenetic pipeline. The alignments can be produced by a choice of four alignment programs and analyzed by a variety of phylogenetic programs. The Hal pipeline connects the programs BLASTP, MCL, user specified alignment programs, GBlocks, ProtTest and user specified phylogenetic programs to produce species trees.
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.
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.
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.
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.