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PhyloPhlAn

A computational pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information.

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.

NeighborNet

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.

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

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.

SDM / Super Distance Matrix

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. It deals with collections offering a large number of source matrices of varying size. This tool applies a distance-based algorithm on the distance supermatrix in order to give a phylogeny. It was tested on a data set of placental mammals.

FlatNJ / FlatNetJoining

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.

SPRDist

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.

HybridNET

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.

HybridCheck

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.

PIRN

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.

LNETWORK

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.

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.

Species Network

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.

MixMapper

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.

QNet / Quartet Network

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.

Network Diversity

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.

Quartet-net

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.

TriLoNet / Trinet Level- one Network algorithm

A Java software package created to construct phylogenetic networks directly from sequence alignments which works by piecing together smaller phylogenetic networks. More specifically, TriLoNet constructs level-1 networks (networks that are somewhat more general than trees) from smaller level-1 networks on three taxa. In simulations, TriLoNet compares well with Lev1athan, a method for reconstructing level-1 networks from three-leaved trees.

BCD Supertrees / Bad Clade Deletion Supertrees

Offers a platform for Maximum-likelihood (ML) analysis dedicated to the rebuilding of large scale phylogeny. BCD Supertrees is an algorithm based on a polynomial time top-down heuristic with the aim of decreasing the number of column deletions of a matric representation (MR). It was tested on several simulated and biological datasets.

PhiPack

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

PhyloNet-HMM

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.

phievo

New

Evolves phenotypic models of cellular processes. phievo is an evolutionary program that randomly combines and optimizes biologically inspired kernels. This application can be used to uncover functional features of existing biological networks, as well as to study the dynamics of evolution of gene networks. It can also represent an alternative to black-box modeling approaches for the understanding of biological networks and their evolution.

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.

snpTree

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 and SNP tree construction from sequencing reads as well as from assembled genomes or contigs. For raw reads, it uses an inhouse toolbox for mapping and genotyping which consists of available programs for next-generation sequencing analysis.

MC-Net

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 from the circular ordering and uses non-negative least squares for weighting splits. One can use SplitsTree program to draw phylogenetic networks from weighted splits.

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.

TripNet / Triplets & 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 work for dense set of rooted triplets, a key innovation is the applicability of TripNet to non-dense set of rooted triplets.

MTRT / Multilabled Tree from Rooted Triplets

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 tested the performance of the MTRT algorithm on more than 400 biological and simulated datasets and showed that MTRT is efficient and can often find the optimal answer in practice.

Ph-CNN / Phylogenetic Convolutional Neural Network

Serves for the classification of metagenomics data. Ph-CNN contains a deep learning (DL) architecture that includes the phylogenetic structure of metagenomics data into the learning process. To perform, the tree structure is used throughout the prediction phase to define the concept of operational taxonomic units (OTUs) neighbours, used in the convolution process by the convolutional neural network (CNN).

Hybroscale

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.

BIMLR

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 resulting network.

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. It also provides a useful addition to the landscape of tools for dissecting and visualizing large numbers of trees. It offers a quick way to visualize and browse the different evolutionary histories.

UBCG / Up-to-date Bacterial Core Gene

Allows generation and evaluation of phylogenetic trees. UBCG is based on the domain-level core genes and canā€™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.

MY-CLOSURE

A software tool for computing supernetworks from partial phylogenetic trees.

UltraNet

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.

TREECON

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 relationship between the distance values. This tool includes different types of programs for several functions: to root the unrooted evolutionary trees; to draw the tree on the screen; and to save the tree.

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.

SuperQ

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 tends to generate results that are in some agreement with Z-closure and Qimputation but with the advantage that a planar split-network is always produced.

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.

BMhyd

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 heritability from its parents. Parameters are estimated by maximum likelihood. Users need to enter a comparative data set, a phylogeny, and information on gene flow leading to hybrids.

FastNN / Fast Neighbor-Net

Consists of a fast implementation of the Neighbor-Net algorithm, a phylogenetic split network algorithm, with a relaxed search strategy. FastNN is a Java program that includes a fast search heuristic called relaxed search inspired by Relaxed Neighbor-Joining and Clearcut. It permits large scale data analysis and bootstrapping.

DivNet

Allows users to perform diversity estimation and to test diversity-related hypothesis. DivNet is an R package proposing a method based on network structure integration making use of the abundance information available from all samples. The application embeds replicate and covariate information and can also being used to assess the relative abundance of a taxon in an ecosystem where it was not observed.

PhaME / Phylogenetic and Molecular Evolution analysis

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 phylogenetic tree. PhaME provides evolutionary analyses (genes under positive selection) using CDS SNPs.

ParSplit

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 to extant values of characters. It estimates cost of splitting a phylogenetic tree at a given node as the integral and over all pairs of asymmetry parameters.

HyDe / Hybridization Detection

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 hybrids within populations. This tool supplies methodology to compute site pattern probabilities and conducting hypothesis tests as well as to parse and analyze genomic data.

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).

Simple Phylogeny

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 aims to model the substitutions that have occurred over evolutionary time and derive and represent the evolutionary relationships between sequences. It uses an alignment directly entered into the input box in a supported format.

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.

Network / Phylogenetic Network Software

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 program. Fast-growing data sizes and enhancement suggestions from the user base motivated the development of two additional software products: DNA Alignment and Network Publisher.

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