Phylogenetic network building software tools | Phylogenomics

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…

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. Source text: Huson and Scornavacca, 2011.

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A Java software package created to construct phylogenetic networks directly…

A Java software package created to construct phylogenetic networks directly from sequence alignments which works by piecing together smaller phylogenetic networks. More specifically, TriLoNet…

An R package for easy detection and dating, and visualisation of recombination,…

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…

Allows to analyze and visualize data. FlatNJ permits the estimation of pendant…

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…

A quartet-based method to construct a phylogenetic network from a multiple…

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…

A method for constructing split networks from weighted quartet trees. QNet can…

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,…

A Java software package allowing the computation and graphical representation…

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…

Includes the option to switch off the scaling of the input trees and also…

Includes the option to switch off the scaling of the input trees and also provides alternatives to objective function. SuperQ represents a method to construct super-networks from partial trees. It…

An interactive method for constructing phylogenetic trees including admixture…

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…

A software package for calculating beta diversity over split systems, a widely…

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)…

Provides a collection of open-source tools and resources for modelling,…

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…

Provides access to phylogenetic tree generation methods from the ClustalW2…

Provides access to phylogenetic tree generation methods from the ClustalW2 package. Simple Phylogeny is an online method to perform basic phylogenetic analysis on a multiple sequence alignment. It…

Provides a general framework for Bayesian inference of reticulate evolution.…

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.…

A phylogenetic and molecular evolution analysis tool. Given a reference, PhaME…

A phylogenetic and molecular evolution analysis tool. Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads, and uses SNP multiple sequence alignment to construct a…

Analyzes the phenotypic evolution of species of hybrid origin on a phylogenetic…

Analyzes the phenotypic evolution of species of hybrid origin on a phylogenetic network. BMhyd can detect the hybrid vigor effect, a burst of variation at formation, and the relative portion of…

There exist some programs for visualizing rooted trees or networks, only few…

There exist some programs for visualizing rooted trees or networks, only few programs for computing and analyzing hybridization networks embedding two bifurcating input trees, and no program,…

Consists of a statistical model and associated inference method for analyzing…

Consists of a statistical model and associated inference method for analyzing complex evolutionary scenarios, especially non-tree-like evolutionary scenarios. PhyloNet-HMM combines phylogenetic…

Relies on the BioPerl bundle and implements several algorithms on phylogenetic…

Relies on the BioPerl bundle and implements several algorithms on phylogenetic networks, from parsing and temporal representation to distances between phylogenetic networks and optimal alignments.…

A heuristic algorithm for the SMRT problem. The goal of MTRT is to construct a…

A heuristic algorithm for the SMRT problem. The goal of MTRT is to construct a minimal MUL tree that is consistent with the input set of triplets and minimizes the number of its duplications. We…

A heuristic algorithm which tries to construct a rooted phylogenetic network…

A heuristic algorithm which tries to construct a rooted phylogenetic network with the minimum number of reticulation nodes from an arbitrary set of rooted triplets. Despite of current methods that…

Reconstructs phylogenetic networks and trees, infers ancestral types and…

Reconstructs phylogenetic networks and trees, infers ancestral types and potential types, evolutionary branchings and variants, and estimates datings. Network includes a data editor and a graphics…

An improved Cass algorithm which can construct a phylogenetic network for a…

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…

A program for constructing a hybridization network with the minimum number of…

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…

A program for reconstructing the most parsimonious phylogenetic networks that…

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…

Computes exact subtree prune and regraft distance. SPRDist uses integer…

Computes exact subtree prune and regraft distance. SPRDist uses integer programming to solve the problem of computing the rooted subtree prune and regraft (rSPR) distances between two rooted binary…

A method for the construction of phylogenetic networks based on Monte-Carlo…

A method for the construction of phylogenetic networks based on Monte-Carlo method. MC-Net finds a circular ordering for taxa, based on Monte-Carlo with simulated annealing, it then extracts splits…

A method for building phylogenetic networks. BIMLR reduces the number of…

A method for building phylogenetic networks. BIMLR reduces the number of constructed networks when the input data order changes. It reduces the number of redundant clusters represented by the…

A package for generating reticulate networks from two or more phylogenetic…

A package for generating reticulate networks from two or more phylogenetic trees. UltraNet utilizes two algorithms for rSPR distance and for hybridization number of two given trees.

A heuristic algorithm based on the simulated annealing as a method for…

A heuristic algorithm based on the simulated annealing as a method for constructing phylogenetic networks from weighted quartets. MCQ.Net finds a circular ordering for taxa and then extracts splits…