With growing exchanges of people and merchandise between countries, epidemics have become an issue of increasing importance and huge amounts of data are being collected every day. Hence, analyses that were usually run in personal computers and desktops are no longer feasible. It is now common to run such tasks in High-performance computing (HPC) environments and/or dedicated systems. On the other hand we are often dealing in these analyses with graphs and trees, and running algorithms to find patterns in such structures. Hence, although graph oriented databases and processing systems can be of much help in this setting, as far as we know there is no solution relying on these technologies to address large scale phylogenetic analysis challenges. This project aims to develop a modular framework for large scale phylogenetic analysis that exploits such technologies, namely Neo4j. We address this challenge by proposing and developing a framework which allows representing large phylogenetic networks and trees, as well as ancillary data, that supports queries on such data, and allows the deployment of algorithms for inferring/detecting patterns and pre-computing visualizations, as a Neo4j plugin. This framework is innovative and brings several advantages to the phylogenetic analysis, such as by storing the phylogenetic trees will avoid having to compute them again, and by using multilayer networks will make the comparison between them more efficient and scalable. Experimental results showcase that it can be very efficient in the mostly used operations and that the supported algorithms comply with their time complexity.
Rearrangement operations transform a phylogenetic tree into another one and hence induce a metric on the space of phylogenetic trees. Popular operations for unrooted phylogenetic trees are NNI (nearest neighbour interchange), SPR (subtree prune and regraft), and TBR (tree bisection and reconnection). Recently, these operations have been extended to unrooted phylogenetic networks, which are generalisations of phylogenetic trees that can model reticulated evolutionary relationships. Here, we study global and local properties of spaces of phylogenetic networks under these three operations. In par…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard. Various heuristics on local search, maximum parsimony, graph cut, etc. lead to different supertree approaches, of which the most popular methods are based on analyzing fixed size subtree topologies (such as triplets or quartets). Time and space complexities of these methods, however, depend on the subtree size considered. Our earlier proposed supertree method …
'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support trees', about which there are numerous algorithmic problems that are important for evolutionary data analysis. Recently, Hayamizu (arXiv:1811.05849 [math.CO]) proved a structure theorem for tree-based phylogenetic networks and obtained linear-time and linear-delay algorithms for many basic problems on support trees, such as counting, optimisation, and enumerat…
Bayesian inference is a popular and widely-used approach to infer phylogenies (evolutionary trees). However, despite decades of widespread application, it remains difficult to judge how well a given Bayesian Markov chain Monte Carlo (MCMC) run explores the space of phylogenetic trees. In this paper, we investigate the Monte Carlo error of phylogenies, focusing on high-dimensional summaries of the posterior distribution, including variability in estimated edge/branch (known in phylogenetics as "split") probabilities and tree probabilities, and variability in the estimated summary tree. Specific…
One regards spaces of trees as stratified spaces, to study distributions of phylogenetic trees. Stratified spaces with may have cycles, however spaces of trees with a fixed number of leafs are contractible. Spaces of trees with three leafs, in particular, are spiders with three legs. One gives an elementary proof of the stickiness of intrinsic sample means on spiders. One also represents four leafs tree data in terms of an associated Petersen graph. One applies such ideas to analyze RNA sequences of SARS-CoV-2 from multiple sources, by building samples of trees and running nonparametric statis…
It is generally accepted that "diversity" is associated with success in evolutionary algorithms. However, diversity is a broad concept that can be measured and defined in a multitude of ways. To date, most evolutionary computation research has measured diversity using the richness and/or evenness of a particular genotypic or phenotypic property. While these metrics are informative, we hypothesize that other diversity metrics are more strongly predictive of success. Phylogenetic diversity metrics are a class of metrics popularly used in biology, which take into account the evolutionary history …
Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks is to develop algorithms for building such networks by amalgamating small networks into a single large network. The level of a phylogenetic network is a measure of its deviation from being a tree; the higher the level of network, the less treelike it becomes. Various algorithms have been developed for building level-1 networks from small networks. However, …
We study the problem of finding a temporal hybridization network for a set of phylogenetic trees that minimizes the number of reticulations. First, we introduce an FPT algorithm for this problem on an arbitrary set of $m$ binary trees with $n$ leaves each with a running time of $O(5^k\cdot n\cdot m)$, where $k$ is the minimum temporal hybridization number. We also present the concept of temporal distance, which is a measure for how close a tree-child network is to being temporal. Then we introduce an algorithm for computing a tree-child network with temporal distance at most $d$ and at most $k…
Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly and to correctly interpret the results of subsequent analyses. BUSCO estimates the completeness and redundancy of processed genomic data based on universal single-copy orthologs. Here we present new functionalities and major improvements of the BUSCO software, as well as the renewal and expansion of the underlying datasets in sync with the OrthoDB v10 release. Among the major novelties, BUSCO now enables phylogenetic placement of the input sequence to automatically select the most appropriat…
Constructing Phylogenetic Networks via Cherry Picking and Machine Learning
University of Trieste（的里雅斯特大学）；Delft Institute of Applied Mathematics（代尔夫特应用数学研究所）；CWI（荷兰国家数学与计算机科学研究中心）；Vrije Universiteit（自由大学）；INRIA-Erable（法国国家信息与自动化研究所Erable团队）
An adaptive time-tree transition kernel for Bayesian phylogenetic inference
KU Leuven（荷语鲁汶大学）；Fred Hutchinson Cancer Center（弗雷德·哈钦森癌症中心）；University of California, Los Angeles（加州大学洛杉矶分校）；David Geffen School of Medicine at UCLA（加州大学洛杉矶分校大卫格芬医学院）；University of Edinburgh（爱丁堡大学）；Getulio Vargas Foundation（热图利奥·瓦加斯基金会）
PhylaFlow: Hybrid Flow Matching in Billera-Holmes-Vogtmann Tree Space for Phylogenetic Inference
Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard（埃里克和wendy Schmidt中心，MIT和哈佛大学Broad研究所）；Department of Biomedical Informatics, Harvard Medical School（哈佛医学院生物医学信息学系）；Centennial High School（Centennial高中）；Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard（传染病与微生物组计划，MIT和哈佛大学Broad研究所）
We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm uses the recently introduced framework of cherry picking sequences and runs in $O((8k)^k \mathrm{poly}(n, t))$ time, where $n$ is the number of leaves of every tree, $t$ is the number of trees, and $k$ is the reticulation number of the constructed network. Moreover, we provide an efficient parallel implementation of the algorithm and show that it can deal with …
TU Delft（代尔夫特理工大学）；Middlesex University（密德萨斯大学）；LIGM, Université Gustave Eiffel（拉格朗日计算与建模实验室，古斯塔夫·埃菲尔大学）；Centre National de Recherche Scientifique（法国国家科学研究中心）
Phylogenetic trees are used to model evolution: leaves are labelled to represent contemporary species ("taxa") and interior vertices represent extinct ancestors. Informally, convex characters are measurements on the contemporary species in which the subset of species (both contemporary and extinct) that share a given state, form a connected subtree. In \cite{KelkS17} it was shown how to efficiently count, list and sample certain restricted subfamilies of convex characters, and algorithmic applications were given. We continue this work in a number of directions. First, we show how combining the…
KTH Royal Institute of Technology（KTH皇家理工学院）；Science for Life Laboratory（生命科学实验室）
Phylogenetics is a classical methodology in computational biology that today has become highly relevant for medical investigation of single-cell data, e.g., in the context of cancer development. The exponential size of the tree space is, unfortunately, a substantial obstacle for Bayesian phylogenetic inference using Markov chain Monte Carlo based methods since these rely on local operations. And although more recent variational inference (VI) based methods offer speed improvements, they rely on expensive auto-differentiation operations for learning the variational parameters. We propose VaiPhy…
Phylogenetic trees are used to model evolution: leaves are labelled to represent contemporary species ("taxa") and interior vertices represent extinct ancestors. Informally, convex characters are measurements on the contemporary species in which the subset of species (both contemporary and extinct) that share a given state, form a connected subtree. Given an unrooted, binary phylogenetic tree T on a set of n >= 2 taxa, a closed (but fairly opaque) expression for the number of convex characters on T has been known since 1992, and this is independent of the exact topology of T. In this note we p…
Comparative and evolutive ecologists are interested in the distribution of quantitative traits among related species. The classical framework for these distributions consists of a random process running along the branches of a phylogenetic tree relating the species. We consider shifts in the process parameters, which reveal fast adaptation to changes of ecological niches. We show that models with shifts are not identifiable in general. Constraining the models to be parsimonious in the number of shifts partially alleviates the problem but several evolutionary scenarios can still provide the sam…
SDSR: A Spectral Divide-and-Conquer Approach for Species Tree Reconstruction
Department of Statistics and Data Science, Hebrew University of Jerusalem（统计与数据科学系，耶路撒冷希伯来大学）；Department of Computer Science and Applied Mathematics, Weizmann Institute of Science（计算机科学与应用数学系，魏茨曼科学研究所）；Department of Applied Mathematics, Tel Aviv University（应用数学系，特拉维夫大学）
