RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss

© The Author(s) 2018. Published by Oxford University Press. RANGER-DTL 2.0 is a software program for inferring gene family evolution using Duplication-Transfer-Loss reconciliation. This new software is highly scalable and easy to use, and offers many new features not currently available in any other reconciliation program. RANGER-DTL 2.0 has a particular focus on reconciliation accuracy and can account for many sources of reconciliation uncertainty including uncertain gene tree rooting, gene tree topological uncertainty, multiple optimal reconciliations and alternative event cost assignments. RANGER-DTL 2.0 is open-source and written in C++ and Python

RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss

© The Author(s) 2018. Published by Oxford University Press. RANGER-DTL 2.0 is a software program for inferring gene family evolution using Duplication-Transfer-Loss reconciliation. This new software is highly scalable and easy to use, and offers many new features not currently available in any other reconciliation program. RANGER-DTL 2.0 has a particular focus on reconciliation accuracy and can account for many sources of reconciliation uncertainty including uncertain gene tree rooting, gene tree topological uncertainty, multiple optimal reconciliations and alternative event cost assignments. RANGER-DTL 2.0 is open-source and written in C++ and Python

Exploring Software Testing Strategies Used on Software Applications in the Government

Developing a defect-free software application is a challenging task. Despite many years of experience, the intense development of reliable software remains a challenge. For this reason, software defects identified at the end of the testing phase are more expensive than those detected sooner. The purpose of this multiple case study is to explore the testing strategies software developers use to ensure the reliability of software applications in the government contracting industry. The target population consisted of software developers from 3 government contracting organizations located along the East Coast region of the United States. Lehman’s laws of software evolution was the conceptual framework. The data collection process included semistructured interviews with software developers (n = 10), including a review of organizational documents (n = 77). Thematic analysis was used to identify patterns and codes from the interviews. Member checking activities were triangulated with organizational documents to produce 4 major themes: (a) communication and collaboration with all stakeholders, (b) development of well-defined requirements, (c) focus on thorough documentation, and (d) focus on automation testing. The results of this study may contribute to information about testing strategies that may help organizations improve or enhance their testing practices. The results of this study may serve as a foundation for positive social change by potentially improving citizens’ experience with government software applications as a result of potential improvement in software testing practice

Genetics of Halophilic Microorganisms

Halophilic microorganisms are found in all domains of life and thrive in hypersaline (high salt content) environments. These unusual microbes have been a subject of study for many years due to their interesting properties and physiology. Studies of the genetics of halophilic microorganisms (from gene expression and regulation to genomics) have provided understanding into the mechanisms of how life can exist at high salinity levels. Here, we highlight recent studies that advance the knowledge of biological function through examination of the genetics of halophilic microorganisms and their viruses