scholarly journals Using RAxML-NG in Practice

Author(s):  
Alexey M. Kozlov ◽  
Alexandros Stamatakis

RAxML-NG is a new phylogentic inference tool that replaces the widely-used RAxML and ExaMLtree inference codes. Compared to its predecessors, RAxML-NG offers improvements in accur-acy, flexibility, speed, scalability, and user-friendliness. In this chapter, we provide practicalrecommendations for the most common use cases of RAxML-NG: tree inference, branch supportestimation via non-parametric bootstrapping, and parameter optimization on a fixed tree topo-logy. We also describe best practices for achieving optimal performance with RAxML-NG, inparticular, with respect to parallel tree inferences on computer clusters and supercomputers. AsRAxML-NG is continuously updated, the most up-to-date version of the tutorial described inthis chapter is available online at: https://cme.h-its.org/exelixis/raxml-ng/tutorial .

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Xiaofeng Steven Liu

Abstract Objectives We introduce a simple and unified methodology to estimate the bias of Pearson correlation coefficients, partial correlation coefficients, and semi-partial correlation coefficients. Methods Our methodology features non-parametric bootstrapping and can accommodate small sample data without making any distributional assumptions. Results Two examples with R code are provided to illustrate the computation. Conclusions The computation strategy is easy to implement and remains the same, be it Pearson correlation or partial or semi-partial correlation.


2015 ◽  
Vol 2015 (1) ◽  
pp. 77-91 ◽  
Author(s):  
Vasile C. Perta ◽  
Marco V. Barbera ◽  
Gareth Tyson ◽  
Hamed Haddadi ◽  
Alessandro Mei

Abstract Commercial Virtual Private Network (VPN) services have become a popular and convenient technology for users seeking privacy and anonymity. They have been applied to a wide range of use cases, with commercial providers often making bold claims regarding their ability to fulfil each of these needs, e.g., censorship circumvention, anonymity and protection from monitoring and tracking. However, as of yet, the claims made by these providers have not received a sufficiently detailed scrutiny. This paper thus investigates the claims of privacy and anonymity in commercial VPN services. We analyse 14 of the most popular ones, inspecting their internals and their infrastructures. Despite being a known issue, our experimental study reveals that the majority of VPN services suffer from IPv6 traffic leakage. The work is extended by developing more sophisticated DNS hijacking attacks that allow all traffic to be transparently captured.We conclude discussing a range of best practices and countermeasures that can address these vulnerabilities


2020 ◽  
Vol 172 ◽  
pp. 11010
Author(s):  
Matthias Winkler ◽  
Bettina Steuri ◽  
Sebastian Stalder ◽  
Florian Antretter

Numerical urban climate models have the potential to be commonly used tools in urban development processes in practice. With integrated modules for building and envelope simulation these complex models allow the assessment of measures in the building sector on the urban climate, e.g. for mitigation of urban heat island effects or preparing for the effects of climate change. However, the currently existing models do not fulfil the requirements that arise in the field of urban planning, as they lack for example functionality, user-friendliness, are hard to integrate in the municipalities’ technical equipment or are not freely available. The German research and development project Urban Climate under Change (2016-2019) developed and validated a new innovative urban climate model called PALM-4U. Aim of the research was to create a model that meets the requirements of users in science as well as practitioners in engineering offices and urban administrations. Therefore, technical features and operational functionalities which the model has to meet to support users in their daily work have been assessed in a first project phase. In total more than 200 requirements were collected which are summed up in the so called “User and Requirements Catalogue”. They served as the basis for testing and evaluating the model’s real-world applicability. To ensure that these complex requirements are met, the whole project follows a transdisciplinary approach integrating science (model development and data assimilation) and practice (user requirements, testing and evaluation) applying a living lab approach: Stakeholders from participating cities and companies took part in on-site workshops, introducing the model with practical use-cases. Afterwards, participants were given tasks covering different features of the model’s applications, which they tested in personal use. The model fulfils the majority of the tested requirements and the users appreciated the model’s concept and functionality. But further development is necessary to provide the practitioners a tool that is applicable in their daily work: Preparation of input data, a user-friendly graphical user-interface, enhanced interfaces to other software and planning tools, use cases that were prepared from experts as well as guidelines and tools for result assessment and interpretation were main suggestions for improvement..


2015 ◽  
Vol 12 (4) ◽  
pp. 046026 ◽  
Author(s):  
John S Butler ◽  
Anna Molloy ◽  
Laura Williams ◽  
Okka Kimmich ◽  
Brendan Quinlivan ◽  
...  

2003 ◽  
Vol 1 (2) ◽  
pp. 69-81
Author(s):  
Manoj Tharian

One Of the major problems with most business engineering efforts, is frat the software engineering and the business engineering community do not communicate properly With each other. This leads to that the Output from business engineering is not used properly as input to the software development effort, and viceversc. The Rational Unified Process addresses this by providing a common language and process for both communities, cs we" os showing how to create and maintain direct traceability between and soft-wore rnodels. In Business Modeling we document business processes using so called business use cases. This assures a common understanding among a" stakeholders Of What business process needs to be supported in the organization. The business use cases cre analyzed to understand how the business should support the I O business processes. This is documented in a business object-model. Many projects may choose not do modéing. Requirements The goal Of the Requirements workaow is 'o describe What the system should do and allows the agree on that description. TO achieve


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