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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…
PhiPack
Desktop

PhiPack

Allows user to work on recombination. PhiPack is useful to treat large…

Allows user to work on recombination. PhiPack is useful to treat large alignments with hundreds of sequences.

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…

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…

FlatNJ
Desktop

FlatNJ FlatNetJoining

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…

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…

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,…

G T A T C G C T A
snpTree
Web

snpTree

Provides an online pipeline which intregrate available single nucletide…

Provides an online pipeline which intregrate available single nucletide polymorphisms (SNPs) analysis softwares with customized scripts. snpTree is a web application for online-automatic SNP analysis…

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…

SuperQ
Desktop

SuperQ

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…

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…

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)…

HyDe
Desktop

HyDe Hybridization Detection

Allows detection of hybridization using phylogenetic invariants. HyDe provides…

Allows detection of hybridization using phylogenetic invariants. HyDe provides methods to detect hybridization at both the population and individual levels and other features to discover individual…

MGUPGMA
Algorithm

MGUPGMA Multiple Graphics Unweighted Pair Group Method with Arithmetic Mean and Neighbor Joining

Enhances the computational performance of constructing a phylogenetic tree from…

Enhances the computational performance of constructing a phylogenetic tree from a huge amount of sequences. MGUPGMA is an Unweighted Pair Group Method with Arithmetic Mean (UPGMA) algorithm, based on…

ParSplit
Desktop

ParSplit

Allows user to identify evolutionary shifts detected from methods based on…

Allows user to identify evolutionary shifts detected from methods based on stochastic models of evolution. ParSplit is a software performing the parsimonious split of a phylogenetic tree with regard…

SPECTRE
Desktop

SPECTRE Suite of PhylogEnetiC Tools for Reticulate Evolution

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…

Simple…
Web

Simple Phylogeny

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…

Species Network
Desktop

Species Network

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.…

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…

SPRDist
Desktop

SPRDist

Solves the rooted Subtree Prune and Regraft (rSPR) distance problem for many…

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…

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,…

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…

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.…

PhyBin
Desktop

PhyBin

Assists in classification of Newick tree files by considering topology. PhyBin…

Assists in classification of Newick tree files by considering topology. PhyBin allows user to browse through the most common tree topologies. it can serve as a component in many genomics pipelines.…

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…

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…

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…

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.

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…

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…

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…

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…

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.

Decaf+py
Desktop

Decaf+py DistancE Calculation using Alignment-Free methods in Python

Discovers and classifies regulatory sequences. Decaf+py is an alignment-free…

Discovers and classifies regulatory sequences. Decaf+py is an alignment-free method based on patterns in sequences. It is able to retrieve regions of similarity occurring in two or more sequences,…

BeeTLe
Desktop

BeeTLe Better Treelength

Analyzes a large number of simulated and biological datasets. BeeTLe is a…

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…

TREECON
Desktop

TREECON

Aims to construct and draw phylogenetic trees. TREECON offers functions to…

Aims to construct and draw phylogenetic trees. TREECON offers functions to compute the evolutionary distance for all pairs of organisms or sequences. It infers a phylogenetic tree by considering the…

DendroUPGMA
Web

DendroUPGMA Dendrogram Unweighted Pair Group Method with Arithmetic mean

Allows user to create a dendrogram from a distance matrix, a set of variables…

Allows user to create a dendrogram from a distance matrix, a set of variables or a similarity matrix. DendroUPGMA can realize different actions such as: computation of a a similarity matrix (only for…

SDM
Web

SDM Super Distance Matrix

Transforms the source matrices without modifying their topological message to…

Transforms the source matrices without modifying their topological message to create phylogenies from large sets of homologous gene. SDM brings the source matrices as close as possible to each other.…

PoInTree
Desktop

PoInTree Polar and Interactive Tree

Constructs and represents phylogenetic trees in a graphical manner. PoInTree…

Constructs and represents phylogenetic trees in a graphical manner. PoInTree permits users to visualize and calculate the distances between two leaves. It employs a space optimization algorithm that…

CINPER
Web

CINPER CSBL INteractive Pathway BuildER

Allows prediction of a user-specified pathway in a prokaryote. CINPER is an…

Allows prediction of a user-specified pathway in a prokaryote. CINPER is an interactive web-based platform for gene network prediction. The software is designed to help minimizing the manual work by…

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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