Introduction

Thank you for using SEGUL! 🙏🏻

SEGUL (SEquence and Genomic UtiLities) is a fast, memory-efficient tool for phylogenomic datasets, from a few Sanger loci to thousands of loci across hundreds of samples. It runs on phones, tablets, desktops, and computing clusters. For an independent review, see the Chan 2024 perspective.

What's new

SEGUI v1.2.0

The redesigned SEGUI app is available now on Google Play, the Microsoft Store, and the Snap Store, and rolling out to the App Store. See GUI installation.

New interface: a searchable tool catalog, suggested workflows, and layouts for phones, tablets, and large screens.
New tools: genetic distance, alignment trimming and unaligning, MAF conversion and summary, and sequence addition, filtering, and transposition.
Viewers and reports: an alignment viewer for large alignments, and interactive reports for read, alignment, and distance summaries.
Inputs and outputs: open folders and .zip or .tar.gz archives, and export output as archives.

See the SEGUI release notes for all changes.

SEGUL v0.25.0

Terminal viewers: segul view align opens alignments in an interactive viewer, and segul view summary browses summary reports as tables and charts.
Charts and reports: summary commands write PNG or SVG charts with --plot. segul align summary and segul align distance also write JSON reports.
Read summary: segul read summary adds read length N50, Q20 and Q30 bases, and, in complete mode, duplication, overrepresented sequences, and adapter content. It is about 12× faster in complete mode.
FASTQ input: quality offsets and gzip or BGZF compression are detected from the reads, and PacBio HiFi quality scores are supported.

Platform support

You can also compile the CLI from source for any platform Rust supports.

Find your way

Quick startFrom install to a first run.

InstallationGUI, CLI, and API setup.

GUI usageDesktop and mobile app guides.

CLI usageTerminal commands and options.

API usagePython, Rust, and R libraries.

FeaturesHow each feature works.

SupportQuestions, issues, and feedback.

Each feature page stands on its own, but start with the introduction of your interface's section for input, output, and data type basics.

Citation

Handika, H., and J. A. Esselstyn. 2024. SEGUL: Ultrafast, memory-efficient and mobile-friendly software for manipulating and summarizing phylogenomic datasets. Molecular Ecology Resources, 24(7). https://doi.org/10.1111/1755-0998.13964.

No access to the article? Request a copy on ResearchGate.

Acknowledgments

We thank Andre E. Moncrieff, Austin S. Chipps, Carl R. Hutter, Darwin Morales-Martínez, Diego J. Elias, Giovani Hernández-Canchola, Glaucia C. Del-Rio, Roberta C. Canton, Samantha L. Rutledge, Sarin Tiatragul, and Spenser J. Babb-Biernacki for feedback on the app and its documentation, and Spenser J. Babb-Biernacki for suggesting the expansion of the SEGUL acronym. Funding came from the National Science Foundation (DEB-1754393 and DEB-2244754) and the Alfred L. Gardner and Mark S. Hafner Mammalogy Fund. Several features are inspired by Phyluce, AMAS, goalign, and FrogCap. SEGUL also builds on excellent open-source libraries from the Rust and Flutter communities.