A broad survey of DNA sequence data simulation tools

S Alosaimi, A Bandiang, N van Biljon… - Briefings in …, 2020 - academic.oup.com
In silico DNA sequence generation is a powerful technology to evaluate and validate
bioinformatics tools, and accordingly more than 35 DNA sequence simulation tools have …

Comparison of methods for picking the operational taxonomic units from amplicon sequences

ZG Wei, XD Zhang, M Cao, F Liu, Y Qian… - Frontiers in …, 2021 - frontiersin.org
With the advent of next-generation sequencing technology, it has become convenient and
cost efficient to thoroughly characterize the microbial diversity and taxonomic composition in …

AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data

JM Silva, W Qi, AJ Pinho, D Pratas - GigaScience, 2023 - academic.oup.com
Background Low-complexity data analysis is the area that addresses the search and
quantification of regions in sequences of elements that contain low-complexity or repetitive …

Benchmarking the topological accuracy of bacterial phylogenomic workflows using in silico evolution

BCL van der Putten, NAH Huijsmans… - Microbial …, 2022 - microbiologyresearch.org
Phylogenetic analyses are widely used in microbiological research, for example to trace the
progression of bacterial outbreaks based on whole-genome sequencing data. In practice …

jackalope: A swift, versatile phylogenomic and high‐throughput sequencing simulator

LA Nell - 2020 - Wiley Online Library
High‐throughput sequencing (HTS) is central to the study of population genomics and has
an increasingly important role in constructing phylogenies. Choices in research design for …

jackalope: a swift, versatile phylogenomic and high-throughput sequencing simulator

LA Nell - bioRxiv, 2019 - biorxiv.org
High-throughput sequencing (HTS) is central to the study of population genomics and has
an increasingly important role in constructing phylogenies. Choices in research design for …