The evolutionary history of a set of species is usually described by a rooted phylogenetic tree. Although it is generally undisputed that bifurcating speciation events and descent with modifications are major forces of evolution, there is a growing belief that reticulate events also have a role to play. Phylogenetic networks provide an alternative to phylogenetic trees and may be more suitable for data sets where evolution involves significant amounts of reticulate events, such as hybridization, horizontal gene transfer, or recombination.
A Java software package allowing the computation and graphical representation of reticulate networks from (a collection of) multi-labeled trees. If a collection of trees are loaded, the software first performs a consensus from which a collection of consensus trees are constructed. Finally, one of the consensus trees can be used to construct a reticulate network. In case a single tree is loaded, the consensus stage is skipped and the reticulate network is constructed directly from that tree. A range of user specified options are provided for both the consensus and network construction methods.
Builds phylogenetic networks for evolutionary analyzing. NeighborNet is an algorithm offering a distance-based method derived from the Neighbor-Joining approach. It exploits similar selection and reduction formulae and is consistent for all circular distance matrices. The algorithm allows users to build split networks from distance measurements and has been implemented in various software such as SplitsTree.
Calculates 28 alignment free dissimilarity measures. CAFE allows visualization of pairwise dissimilarity measures, including dendrograms, heatmap, principal coordinate analysis and network display. It allows the user to study the relationships among genomes and metagenomes. The tool is based on a k-mer alignment-free method and contains 10 conventional measures based on k-mer counts. It also integrates 15 measures based on presence/absence of k-mers.
Allows to analyze, compare, and visualize next generation sequencing (NGS) data. CLC Genomics Workbench offers a complete and customizable solution for genomics, transcriptomics, epigenomics, and metagenomics. The software enables to generate custom workflows, which can combine quality control steps, adapter trimming, read mapping, variant detection, and multiple filtering and annotation steps into a pipeline.
Allows to analyze and visualize data. FlatNJ permits the estimation of pendant edge lengths and allows internal vertices in the network to be labeled. It provides the option to produce a network that is not a tree or an outer-labeled network and it offers an opportunity for exploratory data analysis. It can be used as the basis for developing new methods to better understand data sets involving specific considerations.
Solves the rooted Subtree Prune and Regraft (rSPR) distance problem for many datasets. SPRDist is a method that uses integer programming to resolve the problem of computing rSPR distances between two rooted binary trees. This application takes two binary phylogenetic trees and computes the smallest number of (SPR) operations that transform one tree to the other. It only uses a publicly available integer linear programming (ILP) solver.
A program for constructing a hybridization network with the minimum number of reticulate vertices from two input trees. HybridNet outputs an MAAF (respectively, MAF) by printing out the leaf sets of the trees in the MAAF (respectively, MAF), while it outputs a hybridization network in its extended Newick format. When OPTION is MAAFs (respectively, MAFs), HybridNet outputs the MAAFs (respectively, MAFs) without repetition.
Alleviates the theoretical and technical shortcomings of Poisson Tree Processes (PTP), a phylogeny-aware approach. mPTP incorporates different levels of intraspecific genetic diversity deriving from differences in either the evolutionary history or sampling of each species. It attains a speedup of at least five orders of magnitude compared to PTP, allowing it to delimit species in large (meta-) barcoding data. The tool is designed for analyzing barcoding loci, but can potentially be applied to entire organelle phylogenies.
An R package for easy detection and dating, and visualisation of recombination, introgression and hybridisation events in genomes. HybridCheck can be used to analyse recombination, genetic introgression, hybridisation and horizontal gene transfer. It can scan large (multiple kb) contigs and whole genome sequences of three or more individuals. HybridCheck implements several ABBA-BABA tests and visualises the effects of hybridisation and the resulting mosaic-like genome structure in high-density graphics. The package also reports: (1) the breakpoint positions, (2) the number of mutations in each introgressed block, (3) the probability that the identified region is not caused by recombination, and (4) the estimated age of each recombination event.
A program for reconstructing the most parsimonious phylogenetic networks that contain a set of given phylogenetic trees. One motivation is that the trees are the gene trees and the phylogenetic networks model what may have happen when there is horizontal gene transfer. PIRN outputs a graphical representation of the inferred network.
An improved Cass algorithm which can construct a phylogenetic network for a given set of clusters. We show that LNETWORK is significantly faster than Cass and effectively weakens the influence of input data order. Moreover, we show that LNETWORK can construct a much simpler network than most of the other available methods.
Serves for gene tree error correction in the presence of horizontal gene transfer. TreefixDTL consists of a method able to model gene duplications, horizontal gene transfers, and losses. It can balance sequence likelihood with topological information from a known species tree by utilizing a statistical hypothesis testing framework named Shimodaira–Hasegawa test. It contains features for studying variations in species tree sizes, alignment lengths, rates of duplication, and species tree errors.
Provides a collection of open-source tools and resources for modelling, understanding and visualizing reticulate evolution based on planar split networks. SPECTRE enables bioinformaticians to test and compare methods in order to infer planar split networks. It helps computer scientists build their own methods for inferring phylogenetic networks by reusing our existing data structures and algorithms via the opensource library.
Performs evolutionary analyses of allele frequency data. POPTREE2 can compute various types of genetic distance and construct phylogenetic trees of populations using the neighbor-joining (NJ) method and the unweighted pair-group method with arithmetic mean (UPGMA). Several options are available for computing genetic distances and other statistical quantities.
Provides a general framework for Bayesian inference of reticulate evolution. Species Network is a Bayesian approach to jointly infer species networks and gene trees from multilocus sequence data. This method was implemented in the BEAST 2 package to take advantage of many standard phylogenetic models, such as different substitution models, relaxed molecular clock models, and the BEAUTi graphical interface.
An interactive method for constructing phylogenetic trees including admixture events using single nucleotide polymorphism (SNP) genotype data. MixMapper implements a novel two-phase approach to admixture inference using moment statistics, first building an unadmixed scaffold tree and then adding admixed populations by solving systems of equations that express allele frequency divergences in terms of mixture parameters. Importantly, all features of the model, including topology, sources of gene flow, branch lengths, and mixture proportions, are optimized automatically from the data and include estimates of statistical uncertainty. MixMapper also uses a new method to express branch lengths in easily interpretable drift units.
A method for constructing split networks from weighted quartet trees. QNet can be viewed as a quartet analogue of the distance-based Neighbor-Net (NNet) method for network construction. Just as NNet, QNet works by agglomeratively computing a collection of circular weighted splits of the taxa set which is subsequently represented by a planar split network.
A quartet-based method to construct a phylogenetic network from a multiple sequence alignment. Unlike distances that only reflect the relationship between a pair of taxa, quartets contain information on the relationships among four taxa; these quartets provide adequate capacity to infer a more accurate phylogenetic network. In applications to simulated and biological data sets, we demonstrate that this novel method is robust and effective in reconstructing reticulate evolutionary events and it has the potential to infer more accurate phylogenetic distances than other conventional phylogenetic network construction methods such as Neighbor-Joining, Neighbor-Net, and Split Decomposition. Quartet-net can be used in constructing phylogenetic networks from simple evolutionary events involving a few reticulate events to complex evolutionary histories involving a large number of reticulate events.
A software package for calculating beta diversity over split systems, a widely used class of implicit phylogenetic networks. Network Diversity, provides 11 qualitative (presence-absence, unweighted) and 14 quantitative (weighted) network-based measures of community similarity that model different aspects of community richness and evenness.