scholarly journals Benchmarking of alignment-free sequence comparison methods

2019 ◽  
Author(s):  
Andrzej Zielezinski ◽  
Hani Z. Girgis ◽  
Guillaume Bernard ◽  
Chris-Andre Leimeister ◽  
Kujin Tang ◽  
...  
Keyword(s):  
Sequence Comparison ◽  
Regulatory Element ◽  
Gene Tree ◽  
Species Trees ◽  
Data Types ◽  
Data Intensive ◽  
Current State ◽  
Alignment Free ◽  
Tree Inference ◽  
Data Intensive Applications

ABSTRACTAlignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment. Here, we present a community resource (http://afproject.org) to establish standards for comparing alignment-free approaches across different areas of sequence-based research. We characterize 74 AF methods available in 24 software tools for five research applications, namely, protein sequence classification, gene tree inference, regulatory element detection, genome-based phylogenetic inference and reconstruction of species trees under horizontal gene transfer and recombination events. The interactive web service allows researchers to explore the performance of alignment-free tools relevant to their data types and analytical goals. It also allows method developers to assess their own algorithms and compare them with current state-of-the-art tools, accelerating the development of new, more accurate AF solutions.

scholarly journals Consistency of SVDQuartets and Maximum Likelihood for Coalescent-Based Species Tree Estimation

2020 ◽  
Vol 70 (1) ◽  
pp. 33-48 ◽  
Author(s):  
Matthew Wascher ◽  
Laura Kubatko
Keyword(s):  
Maximum Likelihood ◽  
Gene Tree ◽  
Species Tree ◽  
Gene Trees ◽  
Data Types ◽  
Multispecies Coalescent ◽  
Consistency Results ◽  
True Tree ◽  
Tree Inference ◽  
Statistical Consistency

Abstract Numerous methods for inferring species-level phylogenies under the coalescent model have been proposed within the last 20 years, and debates continue about the relative strengths and weaknesses of these methods. One desirable property of a phylogenetic estimator is that of statistical consistency, which means intuitively that as more data are collected, the probability that the estimated tree has the same topology as the true tree goes to 1. To date, consistency results for species tree inference under the multispecies coalescent (MSC) have been derived only for summary statistics methods, such as ASTRAL and MP-EST. These methods have been found to be consistent given true gene trees but may be inconsistent when gene trees are estimated from data for loci of finite length. Here, we consider the question of statistical consistency for four taxa for SVDQuartets for general data types, as well as for the maximum likelihood (ML) method in the case in which the data are a collection of sites generated under the MSC model such that the sites are conditionally independent given the species tree (we call these data coalescent independent sites [CIS] data). We show that SVDQuartets is statistically consistent for all data types (i.e., for both CIS data and for multilocus data), and we derive its rate of convergence. We additionally show that ML is consistent for CIS data under the JC69 model and discuss why a proof for the more general multilocus case is difficult. Finally, we compare the performance of ML and SDVQuartets using simulation for both data types. [Consistency; gene tree; maximum likelihood; multilocus data; hylogenetic inference; species tree; SVDQuartets.]

scholarly journals TREEasy: an automated workflow to infer gene trees, species trees, and phylogenetic networks from multilocus data

2019 ◽  
Author(s):  
Yafei Mao ◽  
Siqing Hou ◽  
Evan P. Economo
Keyword(s):  
Tree Species ◽  
Network Inference ◽  
Gene Tree ◽  
Phylogenetic Network ◽  
Handling Time ◽  
Phylogenetic Networks ◽  
Recent Analysis ◽  
Gene Trees ◽  
Species Trees ◽  
Tree Inference

AbstractMultilocus genomic datasets can be used to infer a rich set of information about the evolutionary history of a lineage, including gene trees, species trees, and phylogenetic networks. However, user-friendly tools to run such integrated analyses are lacking, and workflows often require tedious reformatting and handling time to shepherd data through a series of individual programs. Here, we present a tool written in Python—TREEasy—that performs automated sequence alignment (with MAFFT), gene tree inference (with IQ-Tree), species inference from concatenated data (with IQ-Tree), species tree inference from gene trees (with ASTRAL, MP-EST, and STELLS2), and phylogenetic network inference (with SNaQ and PhyloNet). The tool only requires FASTA files and nine parameters as inputs. The Tool can be run as command line or through a Graphical User Interface (GUI). As examples, we reproduced a recent analysis of staghorn coral evolution, and performed a new analysis on the evolution of the WGD clade of yeast. The latter revealed novel inferences that were not identified by previous analyses. TREEasy represents a reliable and simple tool to accelerate research in systematic biology (https://github.com/MaoYafei/TREEasy).

scholarly journals The Implications of Over-Estimating Gene Tree Discordance on a Rapid-Radiation Species Tree (Blattodea: Blaberidae)

2019 ◽  
Author(s):  
Dominic A. Evangelista ◽  
Michael A. Gilchrist ◽  
Frédéric Legendre ◽  
Brian O’Meara
Keyword(s):  
Gene Tree ◽  
Predictive Ability ◽  
Species Tree ◽  
Gene Trees ◽  
Species Trees ◽  
Rapid Radiation ◽  
Tree Inference ◽  
Tree Topologies ◽  
Gene Tree Discordance ◽  
Support Relationships

AbstractPatterns of discordance between gene trees and the species trees they reside in are crucial to the debate over the superiority of coalescent or concatenation approaches to tree inference. However, errors in estimating gene tree topologies obfuscate the issue by making gene trees appear erroneously discordant with the species tree. We thus test the prevalence of discordance between gene trees and their species tree using an empirical dataset for a clade with a rapid radiation (Blaberidae). We find that one model of codon evolution (FMutSel0) prefers gene trees that are less discordant, while another (SelAC) shows no such preference. We compare the species trees resulting from the selected sets of gene trees on the basis of internal consistency, predictive ability, and congruence with independent data. The species tree resulting from gene trees those chosen by FMutSel0, a set with low discordance, is the most robust and biologically plausible. Thus, we conclude that the results from FMutSel0 are better supported: simple models (i.e., GTR and ECM) infer trees with erroneously high levels of gene tree discordance. Furthermore, the amount of discordance in the set of gene trees has a large effect on the downstream phylogeny. Thus, decreasing gene tree error by lessening erroneous discordance can result in higher quality species trees. These results allow us to support relationships among blaberid cockroaches that were previously in flux as they now demonstrate molecular and morphological congruence.

scholarly journals 6G Enabled Smart Infrastructure for Sustainable Society: Opportunities, Challenges, and Research Roadmap

Sensors ◽  
2021 ◽  
Vol 21 (5) ◽  
pp. 1709
Author(s):  
Agbotiname Lucky Imoize ◽  
Oluwadara Adedeji ◽  
Nistha Tandiya ◽  
Sachin Shetty
Keyword(s):  
Wireless Communication ◽  
Psychological Health ◽  
Future Research ◽  
Agriculture Education ◽  
Social Psychological ◽  
Research Issues ◽  
Data Intensive ◽  
Wireless Communication Network ◽  
Data Intensive Applications

The 5G wireless communication network is currently faced with the challenge of limited data speed exacerbated by the proliferation of billions of data-intensive applications. To address this problem, researchers are developing cutting-edge technologies for the envisioned 6G wireless communication standards to satisfy the escalating wireless services demands. Though some of the candidate technologies in the 5G standards will apply to 6G wireless networks, key disruptive technologies that will guarantee the desired quality of physical experience to achieve ubiquitous wireless connectivity are expected in 6G. This article first provides a foundational background on the evolution of different wireless communication standards to have a proper insight into the vision and requirements of 6G. Second, we provide a panoramic view of the enabling technologies proposed to facilitate 6G and introduce emerging 6G applications such as multi-sensory–extended reality, digital replica, and more. Next, the technology-driven challenges, social, psychological, health and commercialization issues posed to actualizing 6G, and the probable solutions to tackle these challenges are discussed extensively. Additionally, we present new use cases of the 6G technology in agriculture, education, media and entertainment, logistics and transportation, and tourism. Furthermore, we discuss the multi-faceted communication capabilities of 6G that will contribute significantly to global sustainability and how 6G will bring about a dramatic change in the business arena. Finally, we highlight the research trends, open research issues, and key take-away lessons for future research exploration in 6G wireless communication.

scholarly journals EZIOTracer

2021 ◽  
Vol 55 (1) ◽  
pp. 88-98
Author(s):  
Mohammed Islam Naas ◽  
François Trahay ◽  
Alexis Colin ◽  
Pierre Olivier ◽  
Stéphane Rubini ◽  
...  
Keyword(s):  
Analysis Framework ◽  
Comprehensive Understanding ◽  
Kernel Space ◽  
Data Intensive ◽  
Storage Performance ◽  
Performance Requirements ◽  
Memory Footprint ◽  
Extreme Performance ◽  
Data Intensive Applications ◽  
Kernel Level

Tracing is a popular method for evaluating, investigating, and modeling the performance of today's storage systems. Tracing has become crucial with the increase in complexity of modern storage applications/systems, that are manipulating an ever-increasing amount of data and are subject to extreme performance requirements. There exists many tracing tools focusing either on the user-level or the kernel-level, however we observe the lack of a unified tracer targeting both levels: this prevents a comprehensive understanding of modern applications' storage performance profiles. In this paper, we present EZIOTracer, a unified I/O tracer for both (Linux) kernel and user spaces, targeting data intensive applications. EZIOTracer is composed of a userland as well as a kernel space tracer, complemented with a trace analysis framework able to merge the output of the two tracers, and in particular to relate user-level events to kernel-level ones, and vice-versa. On the kernel side, EZIOTracer relies on eBPF to offer safe, low-overhead, low memory footprint, and flexible tracing capabilities. We demonstrate using FIO benchmark the ability of EZIOTracer to track down I/O performance issues by relating events recorded at both the kernel and user levels. We show that this can be achieved with a relatively low overhead that ranges from 2% to 26% depending on the I/O intensity.

scholarly journals Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere

2020 ◽  
Author(s):  
Fernando Lopes ◽  
Larissa R Oliveira ◽  
Amanda Kessler ◽  
Yago Beux ◽  
Enrique Crespo ◽  
...  
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Molecular Data ◽  
Species Tree ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Data Types ◽  
High Coverage ◽  
Sea Lions ◽  
The Family

Abstract The phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance because of strong gene-tree species tree discordance. Divergence times estimates in the group also vary largely between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events occurred. Here we used high-coverage genome-wide sequencing for 14 of the 15 species of Otariidae to elucidate the phylogeny of the family and its bearing on the taxonomy and biogeographical history. Despite extreme topological discordance among gene trees, we found a fully supported species tree that agrees with the few well-accepted relationships and establishes monophyly of the genus Arctocephalus. Our data support a relatively recent trans-hemispheric dispersal at the base of a southern clade, which rapidly diversified into six major lineages between 3 to 2.5 Ma. Otaria diverged first, followed by Phocarctos and then four major lineages within Arctocephalus. However, we found Zalophus to be non-monophyletic, with California (Z. californianus) and Steller sea lions (Eumetopias jubatus) grouping closer than the Galapagos sea lion (Z. wollebaeki) with evidence for introgression between the two genera. Overall, the high degree of genealogical discordance was best explained by incomplete lineage sorting resulting from quasi-simultaneous speciation within the southern clade with introgresssion playing a subordinate role in explaining the incongruence among and within prior phylogenetic studies of the family.

Extraction of high quality k-words for alignment-free sequence comparison

2014 ◽  
Vol 358 ◽  
pp. 31-51 ◽  
Author(s):  
Upuli Gunasinghe ◽  
Damminda Alahakoon ◽  
Susan Bedingfield
Keyword(s):  
Sequence Comparison ◽  
High Quality ◽  
Alignment Free
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