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Software, Volume 1, Issue 3

September 2022 - 7 articles

Cover Story: To understand the performance of methods developed for the reconstruction of evolutionary histories of genes and species, it is indispensable to test such methods on reliable benchmark sets. Since the true histories are in almost all cases unknown, simulated data must be used. AsymmeTree is a flexible and easy-to-use Python package for the simulation of gene family and species histories as well as underlying genes. Those histories can be simulated to include common evolutionary mechanisms such as gene duplication, loss, conversion, and horizontal transfer. Different models can be used to generate realistic scenarios. AsymmeTree is freely available and allows the user to interact with, analyse, and possibly manipulate the simulated scenarios. View this paper
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Articles (7)

  • Article
  • Open Access
1 Citations
2,842 Views
17 Pages

5 September 2022

Previous studies reported that reviewers ask questions and engage in discussions during software reviews and that the concerns identified by the questions and discussions help detect defects. Although such concerns about potential defects lead to fin...

  • Article
  • Open Access
17 Citations
11,328 Views
48 Pages

24 August 2022

The key objective of this paper is to investigate the evolution of hybrid software development methods and highlight the main difficulties that arise with regard to information systems (IS) auditing. While technology firms today are under constant pr...

  • Article
  • Open Access
2 Citations
7,105 Views
17 Pages

13 August 2022

With archaic coding techniques, there will be a time when it will be necessary to modernize vulnerable software. However, redeveloping out-of-date code can be a time-consuming task when dealing with a multitude of files. To reduce the amount of reass...

  • Article
  • Open Access
4 Citations
3,908 Views
23 Pages

7 August 2022

AsymmeTree is a flexible and easy-to-use Python package for the simulation of gene family histories. It simulates species trees and considers the joint action of gene duplication, loss, conversion, and horizontal transfer to evolve gene families alon...

  • Article
  • Open Access
19 Citations
23,330 Views
11 Pages

5 August 2022

Agile software development methods were introduced to minimize problems faced using traditional software development approaches. There are several Agile approaches used in developing software projects, these include Scrum, Extreme programming and Kan...

  • Article
  • Open Access
3 Citations
3,595 Views
21 Pages

Selecting Non-Line of Sight Critical Scenarios for Connected Autonomous Vehicle Testing

  • Tanvir Allidina,
  • Lipika Deka,
  • Daniel Paluszczyszyn and
  • David Elizondo

13 July 2022

The on-board sensors of connected autonomous vehicles (CAVs) are limited by their range and inability to see around corners or blind spots, otherwise known as non-line of sight scenarios (NLOS). These scenarios have the potential to be fatal (critica...

  • Article
  • Open Access
1 Citations
7,012 Views
21 Pages

User Story Quality in Practice: A Case Study

  • Mohammad Amin Kuhail and
  • Soren Lauesen

28 June 2022

(1) Background: User stories are widely used in Agile development as requirements. However, few studies have assessed the quality of user stories in practice. (2) Methods: What is the quality of user stories in practice? To answer the research questi...

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Software - ISSN 2674-113X