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Phylogenetic network building software tools

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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PADRE / Package for Analyzing and Displaying Reticulate Evolution
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.
CAFE / aCcelerated Alignment-FrEe sequence analysis
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.
CLC bio / CLC Genomics Workbench
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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.
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.
mPTP / multi-rate Poisson Tree Processes
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 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.
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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.
Consists of a statistical model and associated inference method for analyzing complex evolutionary scenarios, especially non-tree-like evolutionary scenarios. PhyloNet-HMM combines phylogenetic networks, which capture complex evolutionary relationships among genomes, with hidden Markov models, which capture dependencies within genomes, in a novel manner. The performance of PhyloNet-HMM was validated using simulated and empirical data sets that included tree-like and non-tree-like evolutionary scenarios.
CoVennTree / Comparative weighted Venn Tree
Simultaneously compares up to three multifarious datasets by aggregating and propagating information from the bottom to the top level and produces a graphical output in Cytoscape. The underlying concept of CoVennTree is to bring information from the leaf level up to the root node while maintaining the properties of the content of every dataset. With the introduction of weighted Venn structures, the amounts and relationships of data associated with different conditions can be correlated and simultaneously aggregated without losing relevant information. CoVennTree has been integrated into the Galaxy ToolShed and can be directly downloaded and integrated into the user instance.
BeeTLe / Better Treelength
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 total treelength. It produces a set of trees on a given input set of unaligned sequences, uses POY to compute the treelength of each tree, and then returns the tree that had the shortest treelength. It is guaranteed to find trees at least as short as those found using POY, and thus enables to evaluate the impact of using treelength to find trees.
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, however, computing all hybridization networks for an arbitrary number (>2) of multifurcating input trees sharing just an overlapping set of taxa. Hybroscale is specifically designed to combine all of those functionalities that are, obviously, of high interest for the research of reticulation events. It contains a graphical user interface, which enables an easy handling of its algorithms and visualization methods.
UBCG / Up-to-date Bacterial Core Gene
Allows generation and evaluation of phylogenetic trees. UBCG is based on the domain-level core genes and can’t be applied to any taxonomic ranks. The software automatically generates the maximum likelihood trees with gene support index (GSI) values, making this method available for the users who are not skillful in bioinformatics. It was used to infer the phylogenomic relationship among Escherichia and related taxa including the genera Citrobacter, Klebsiella, Salmonella, and Shigella.
Decaf+py / DistancE Calculation using Alignment-Free methods in Python
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, with or without alignment. This tool considers the patterns as local alignments in order to make estimation of phylogenetic distances. It can be useful to determine the maximum-likelihood (ML) distance of reference and automated alignments.
SPECTRE / Suite of PhylogEnetiC Tools for Reticulate Evolution
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.
MGUPGMA / Multiple Graphics Unweighted Pair Group Method with Arithmetic Mean and Neighbor Joining
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 Graphics Processing Unit (GPU)-UPGMA, with multiple GPUs using Compute Unified Device Architecture (CUDA) framework and NVIDIA Collective Communications Library (NCCL). The UPGMA algorithm constructs a phylogenetic tree from the pairwise similarity matrix which describes similarities between all possible pairs of given operational taxonomic units (OTUs).
DendroUPGMA / Dendrogram Unweighted Pair Group Method with Arithmetic mean
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 sets of variables); making a clustering that uses Weighted Pair Group Method with Arithmetic Mean (WPGMA) or Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithm; and transforming similarity coefficients into distances.
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