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…
Quartet-net
Desktop

Quartet-net

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…

Network
Desktop

Network Phylogenetic Network Software

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…

PhaME
Desktop

PhaME Phylogenetic and Molecular Evolution analysis

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…

BMhyd
Desktop

BMhyd

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…

MY-CLOSURE
Desktop

MY-CLOSURE

A software tool for computing supernetworks from partial phylogenetic trees.

A software tool for computing supernetworks from partial phylogenetic trees.

PADRE
Desktop

PADRE Package for Analyzing and Displaying Reticulate Evolution

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…

QNet
Desktop

QNet Quartet Network

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,…

HybridCheck
Desktop

HybridCheck

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…

Hybroscale
Desktop

Hybroscale

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,…

UltraNet
Desktop

UltraNet

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.

MixMapper
Desktop

MixMapper

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…

MTRT
Desktop

MTRT Multilabled Tree from Rooted Triplets

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…

TriLoNet
Desktop

TriLoNet Trinet Level- one Network algorithm

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…

Network…
Desktop

Network Diversity

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)…

PhyloNetwork
Desktop
Web

PhyloNetwork

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.…

BIMLR
Desktop

BIMLR

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…

LNETWORK
Desktop

LNETWORK

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…

MC-Net
Desktop

MC-Net

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…

PhyloNet-HMM
Desktop

PhyloNet-HMM

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…

TripNet
Desktop

TripNet Triplets & Network

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…

HybridNET
Desktop

HybridNET

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…

PIRN
Desktop

PIRN

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…

SPRDist
Desktop

SPRDist

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…

MCQ.Net
Desktop

MCQ.Net Monte-Carlo Quartet Network

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…

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