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SEGUL: An ultrafast, memory-efficient alignment manipulation and summary tool for phylogenomics
  • Heru Handika,
  • Jacob Esselstyn
Heru Handika
Louisiana State University and A&M College

Corresponding Author:[email protected]

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Jacob Esselstyn
Louisiana State University and A&M College
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Abstract

Phylogenetic studies now routinely require manipulating and summarizing thousands of data files. For most of these tasks, currently available software requires considerable computing resources and substantial knowledge of command-line applications. We develop ultrafast and memory-efficient software that performs over a dozen common phylogenomic manipulations and calculates statistics summarizing essential data features. Our software is available as standalone command-line (CLI) and graphical user interface (GUI) applications, and as a programming language library for Rust, R, and Python, with possible support of other languages. The CLI and library versions, SEGUL, run native on Windows, Linux, and macOS, including Apple ARM Macs. The GUI version extends support to include mobile iOS and Android operating systems. SEGUL offer fast execution times and low memory footprints regardless of dataset size and platform choice. The inclusion of a GUI minimizes bioinformatics barriers to phylogenomics while SEGUL’s efficiency reduces economic barriers by enabling analysis on inexpensive hardware. Our support for mobile operating systems further enables teaching phylogenomics where access to computing power is limited.
04 Jul 2023Submitted to Molecular Ecology Resources
06 Jul 2023Submission Checks Completed
06 Jul 2023Assigned to Editor
06 Jul 2023Review(s) Completed, Editorial Evaluation Pending
06 Jul 2023Reviewer(s) Assigned
18 Sep 2023Editorial Decision: Revise Minor
13 Feb 20241st Revision Received
15 Feb 2024Assigned to Editor
15 Feb 2024Submission Checks Completed
15 Feb 2024Review(s) Completed, Editorial Evaluation Pending
08 Mar 2024Editorial Decision: Revise Minor
18 Mar 20242nd Revision Received
19 Mar 2024Submission Checks Completed
19 Mar 2024Assigned to Editor
19 Mar 2024Review(s) Completed, Editorial Evaluation Pending
15 Apr 2024Editorial Decision: Accept