SEGUL comes in two interfaces: a command-line interface (CLI) and a graphical user interface (GUI) . Both run the same core, so they produce the same results.
CLI and GUI at a glance Left: the CLI runs SEGUL from a terminal, for example segul align concat on a folder of NEXUS loci. It is the fastest option, runs on HPC clusters and WSL, is scriptable, and builds from source anywhere Rust runs. Right: the GUI is a desktop and mobile app with a navigation rail, a file picker, and a run button. It needs no command line, includes a text and table viewer, runs on phones and tablets, and guides input and output options. CLI Commands and scripts $ segul align concat \ -d loci/ -f nexus Input 4,060 alignments Output concat.nex ✓ Done in 2.5 s Best for Fastest, smallest memory use Runs on HPC clusters and WSL Scriptable for pipelines Builds from source anywhere Rust runs GUI Point and click Alignment concatenation Input: loci/ · 4,060 files Run Best for No command line needed Built-in text and table viewer Runs on phones and tablets Guided input and output options Both run the same SEGUL core, so results match. Install one or both; they do not interfere. Platform support Linux: CLI supported, GUI supported (GUI needs GLIBC 2.34+; CLI also on ARM64). macOS: CLI supported, GUI supported. Windows: CLI supported, GUI supported. WSL: CLI supported, GUI not supported. iOS: CLI not supported, GUI supported. iPadOS: CLI not supported, GUI supported. Android: CLI partial support, GUI supported (CLI through Termux). CLI GUI DESKTOP Linux GUI needs GLIBC 2.34+; CLI also on ARM64 macOS Windows WSL MOBILE iOS iPadOS Android CLI through Termux Supported Partial Not supported You can also compile the CLI from source for any platform Rust supports. See the GUI and CLI installation guides. For Linux, the CLI comes as a fully static binary for older distributions and a GLIBC-linked binary for newer ones. You can also build the CLI from source .
Feature differences CLI only: --dry-run preview, --npercent cutoffs, Nested input folders, Non-standard extensions. Both: Every alignment task, Every sequence task, Read, contig, and MAF tools, Same output files. GUI only: Text and table viewer, iOS, iPadOS, Android, File picker input, Point-and-click options. CLI only --dry-run preview --npercent cutoffs Nested input folders Non-standard extensions Both Every alignment task Every sequence task Read, contig, and MAF tools Same output files GUI only Text and table viewer iOS, iPadOS, Android File picker input Point-and-click options The main tasks are the same in both. The differences are in how you give input and look at output. Each GUI task group maps to one or more CLI commands:
GUI task groups and CLI commands The GUI Alignment group maps to the CLI commands segul align and segul partition, the latter for partition conversion. The Sequence group maps to segul sequence. The Genomic group maps to segul read for FASTQ reads, segul contig for contigs, and segul maf for MAF files. GUI tasks match CLI subcommands. GUI task group CLI command Alignment segul align segul partition Sequence segul sequence Genomic segul read segul contig segul maf A GUI task is a CLI subcommand, for example Alignment › Concatenation is segul align concat. Learn more about the CLI and GUI options.
The charts below are built from the SEGUL benchmark data (SEGUL v0.20.0). Desktop runs used Linux on an AMD Ryzen 9 5900X. AMAS and goalign are included for comparison. The SEGUL paper describes the methods.
Concatenation execution time Mean execution time to concatenate NEXUS alignments. DNA · Oliveros et al. 2019 · 4,060 loci, 522.5 Mbases: SEGUL CLI · Linux 2.51 s, SEGUL GUI · Linux 3.56 s, SEGUL GUI · iPadOS 6.16 s, SEGUL GUI · Android 16.3 s, AMAS 3.43 s, goalign 7.07 s. Protein · Shen et al. 2018 · 2,408 loci, 398.8 Mbases: SEGUL CLI · Linux 3.88 s, SEGUL GUI · Linux 4.94 s, SEGUL GUI · iPadOS 6.90 s, SEGUL GUI · Android 17.1 s, AMAS 3.54 s, goalign 5.38 s. DNA · Oliveros et al. 2019 · 4,060 loci, 522.5 Mbases 0 5 10 15 20 SEGUL CLI · Linux: 2.51 s ± 0.02 SD (n = 5) SEGUL CLI · Linux 2.51 SEGUL GUI · Linux: 3.56 s ± 0.09 SD (n = 5) SEGUL GUI · Linux 3.56 SEGUL GUI · iPadOS: 6.16 s ± 0.05 SD (n = 5) SEGUL GUI · iPadOS 6.16 SEGUL GUI · Android: 16.3 s ± 0.08 SD (n = 5) SEGUL GUI · Android 16.3 AMAS: 3.43 s ± 0.04 SD (n = 5) AMAS 3.43 goalign: 7.07 s ± 0.08 SD (n = 5) goalign 7.07 Protein · Shen et al. 2018 · 2,408 loci, 398.8 Mbases 0 5 10 15 20 SEGUL CLI · Linux: 3.88 s ± 0.09 SD (n = 5) SEGUL CLI · Linux 3.88 SEGUL GUI · Linux: 4.94 s ± 0.09 SD (n = 5) SEGUL GUI · Linux 4.94 SEGUL GUI · iPadOS: 6.90 s ± 0.46 SD (n = 5) SEGUL GUI · iPadOS 6.90 SEGUL GUI · Android: 17.1 s ± 0.22 SD (n = 5) SEGUL GUI · Android 17.1 AMAS: 3.54 s ± 0.06 SD (n = 5) AMAS 3.54 goalign: 5.38 s ± 0.10 SD (n = 5) goalign 5.38 Execution time (seconds) Shorter is faster. Whiskers show one standard deviation over five runs. Show the numbers Panel App Mean (s) SD Runs DNA · Oliveros et al. 2019 · 4,060 loci, 522.5 Mbases SEGUL CLI · Linux 2.51 0.02 5 DNA · Oliveros et al. 2019 · 4,060 loci, 522.5 Mbases SEGUL GUI · Linux 3.56 0.09 5 DNA · Oliveros et al. 2019 · 4,060 loci, 522.5 Mbases SEGUL GUI · iPadOS 6.16 0.05 5 DNA · Oliveros et al. 2019 · 4,060 loci, 522.5 Mbases SEGUL GUI · Android 16.3 0.08 5 DNA · Oliveros et al. 2019 · 4,060 loci, 522.5 Mbases AMAS 3.43 0.04 5 DNA · Oliveros et al. 2019 · 4,060 loci, 522.5 Mbases goalign 7.07 0.08 5 Protein · Shen et al. 2018 · 2,408 loci, 398.8 Mbases SEGUL CLI · Linux 3.88 0.09 5 Protein · Shen et al. 2018 · 2,408 loci, 398.8 Mbases SEGUL GUI · Linux 4.94 0.09 5 Protein · Shen et al. 2018 · 2,408 loci, 398.8 Mbases SEGUL GUI · iPadOS 6.90 0.46 5 Protein · Shen et al. 2018 · 2,408 loci, 398.8 Mbases SEGUL GUI · Android 17.1 0.22 5 Protein · Shen et al. 2018 · 2,408 loci, 398.8 Mbases AMAS 3.54 0.06 5 Protein · Shen et al. 2018 · 2,408 loci, 398.8 Mbases goalign 5.38 0.10 5
Concatenation peak memory Mean peak memory to concatenate NEXUS alignments on Linux. DNA · Oliveros et al. 2019 · 4,060 loci, 522.5 Mbases: SEGUL CLI · Linux 638 MB, SEGUL GUI · Linux 869 MB, AMAS 2,262 MB, goalign 3,138 MB. Protein · Shen et al. 2018 · 2,408 loci, 398.8 Mbases: SEGUL CLI · Linux 590 MB, SEGUL GUI · Linux 766 MB, AMAS 1,734 MB, goalign 2,106 MB. DNA · Oliveros et al. 2019 · 4,060 loci, 522.5 Mbases 0 1,000 2,000 3,000 4,000 SEGUL CLI · Linux: 638 MB ± 1.43 SD (n = 5) SEGUL CLI · Linux 638 SEGUL GUI · Linux: 869 MB ± 3.89 SD (n = 5) SEGUL GUI · Linux 869 AMAS: 2,262 MB ± 1.34 SD (n = 5) AMAS 2,262 goalign: 3,138 MB ± 290 SD (n = 5) goalign 3,138 Protein · Shen et al. 2018 · 2,408 loci, 398.8 Mbases 0 1,000 2,000 3,000 SEGUL CLI · Linux: 590 MB ± 4.02 SD (n = 5) SEGUL CLI · Linux 590 SEGUL GUI · Linux: 766 MB ± 4.79 SD (n = 5) SEGUL GUI · Linux 766 AMAS: 1,734 MB ± 1.08 SD (n = 5) AMAS 1,734 goalign: 2,106 MB ± 159 SD (n = 5) goalign 2,106 Peak memory (MB) Lower uses less memory. Measured on desktop only; CLI numbers exclude the terminal app. Show the numbers Panel App Mean (MB) SD Runs DNA · Oliveros et al. 2019 · 4,060 loci, 522.5 Mbases SEGUL CLI · Linux 638 1.43 5 DNA · Oliveros et al. 2019 · 4,060 loci, 522.5 Mbases SEGUL GUI · Linux 869 3.89 5 DNA · Oliveros et al. 2019 · 4,060 loci, 522.5 Mbases AMAS 2,262 1.34 5 DNA · Oliveros et al. 2019 · 4,060 loci, 522.5 Mbases goalign 3,138 290 5 Protein · Shen et al. 2018 · 2,408 loci, 398.8 Mbases SEGUL CLI · Linux 590 4.02 5 Protein · Shen et al. 2018 · 2,408 loci, 398.8 Mbases SEGUL GUI · Linux 766 4.79 5 Protein · Shen et al. 2018 · 2,408 loci, 398.8 Mbases AMAS 1,734 1.08 5 Protein · Shen et al. 2018 · 2,408 loci, 398.8 Mbases goalign 2,106 159 5
CLI memory covers only the SEGUL process, not the terminal app it runs in. The GUI is a standalone app, so its numbers include the whole app, including its interface.
SEGUL CLI and GUI across tasks Mean execution time on the Oliveros et al. 2019 DNA dataset for concatenation, conversion, splitting, summary statistics, and sequence removal, comparing the SEGUL CLI on Linux with the GUI on Linux, iPadOS, and Android. The Linux GUI stays close to the CLI; mobile devices take longer, partly because the app copies input files first. Concatenation: SEGUL CLI · Linux 2.51 s, SEGUL GUI · Linux 3.56 s, SEGUL GUI · iPadOS 6.16 s, SEGUL GUI · Android 16.3 s. Conversion: SEGUL CLI · Linux 0.38 s, SEGUL GUI · Linux 0.41 s, SEGUL GUI · iPadOS 4.98 s, SEGUL GUI · Android 3.64 s. Splitting: SEGUL CLI · Linux 3.54 s, SEGUL GUI · Linux 4.82 s, SEGUL GUI · iPadOS 6.60 s, SEGUL GUI · Android 14.5 s. Summary: SEGUL CLI · Linux 1.10 s, SEGUL GUI · Linux 1.20 s, SEGUL GUI · iPadOS 7.70 s, SEGUL GUI · Android 14.2 s. Sequence Removal: SEGUL CLI · Linux 0.43 s, SEGUL GUI · Linux 0.42 s, SEGUL GUI · iPadOS 4.20 s, SEGUL GUI · Android 3.50 s. Concatenation SEGUL CLI · Linux: 2.51 s ± 0.02 SD (n = 5) SEGUL CLI · Linux 2.51 SEGUL GUI · Linux: 3.56 s ± 0.09 SD (n = 5) SEGUL GUI · Linux 3.56 SEGUL GUI · iPadOS: 6.16 s ± 0.05 SD (n = 5) SEGUL GUI · iPadOS 6.16 SEGUL GUI · Android: 16.3 s ± 0.08 SD (n = 5) SEGUL GUI · Android 16.3 Conversion SEGUL CLI · Linux: 0.38 s ± 0.05 SD (n = 5) SEGUL CLI · Linux 0.38 SEGUL GUI · Linux: 0.41 s ± 0.02 SD (n = 5) SEGUL GUI · Linux 0.41 SEGUL GUI · iPadOS: 4.98 s ± 0.83 SD (n = 5) SEGUL GUI · iPadOS 4.98 SEGUL GUI · Android: 3.64 s ± 0.21 SD (n = 5) SEGUL GUI · Android 3.64 Splitting SEGUL CLI · Linux: 3.54 s ± 0.02 SD (n = 5) SEGUL CLI · Linux 3.54 SEGUL GUI · Linux: 4.82 s ± 0.04 SD (n = 5) SEGUL GUI · Linux 4.82 SEGUL GUI · iPadOS: 6.60 s ± 0.19 SD (n = 5) SEGUL GUI · iPadOS 6.60 SEGUL GUI · Android: 14.5 s ± 0.74 SD (n = 5) SEGUL GUI · Android 14.5 Summary SEGUL CLI · Linux: 1.10 s ± 0.00 SD (n = 5) SEGUL CLI · Linux 1.10 SEGUL GUI · Linux: 1.20 s ± 0.01 SD (n = 5) SEGUL GUI · Linux 1.20 SEGUL GUI · iPadOS: 7.70 s ± 0.25 SD (n = 5) SEGUL GUI · iPadOS 7.70 SEGUL GUI · Android: 14.2 s ± 0.11 SD (n = 5) SEGUL GUI · Android 14.2 Sequence Removal 0 5 10 15 20 SEGUL CLI · Linux: 0.43 s ± 0.02 SD (n = 5) SEGUL CLI · Linux 0.43 SEGUL GUI · Linux: 0.42 s ± 0.02 SD (n = 5) SEGUL GUI · Linux 0.42 SEGUL GUI · iPadOS: 4.20 s ± 0.10 SD (n = 5) SEGUL GUI · iPadOS 4.20 SEGUL GUI · Android: 3.50 s ± 0.07 SD (n = 5) SEGUL GUI · Android 3.50 Execution time (seconds) DNA dataset (Oliveros et al. 2019). All tasks share one scale. Show the numbers Panel App Mean (s) SD Runs Concatenation SEGUL CLI · Linux 2.51 0.02 5 Concatenation SEGUL GUI · Linux 3.56 0.09 5 Concatenation SEGUL GUI · iPadOS 6.16 0.05 5 Concatenation SEGUL GUI · Android 16.3 0.08 5 Conversion SEGUL CLI · Linux 0.38 0.05 5 Conversion SEGUL GUI · Linux 0.41 0.02 5 Conversion SEGUL GUI · iPadOS 4.98 0.83 5 Conversion SEGUL GUI · Android 3.64 0.21 5 Splitting SEGUL CLI · Linux 3.54 0.02 5 Splitting SEGUL GUI · Linux 4.82 0.04 5 Splitting SEGUL GUI · iPadOS 6.60 0.19 5 Splitting SEGUL GUI · Android 14.5 0.74 5 Summary SEGUL CLI · Linux 1.10 0.00 5 Summary SEGUL GUI · Linux 1.20 0.01 5 Summary SEGUL GUI · iPadOS 7.70 0.25 5 Summary SEGUL GUI · Android 14.2 0.11 5 Sequence Removal SEGUL CLI · Linux 0.43 0.02 5 Sequence Removal SEGUL GUI · Linux 0.42 0.02 5 Sequence Removal SEGUL GUI · iPadOS 4.20 0.10 5 Sequence Removal SEGUL GUI · Android 3.50 0.07 5
For long jobs, the interface makes little difference. Summarizing a whole-genome FASTQ sample took about the same time in both. Part of the memory gap is the GUI's own interface, as noted above:
SEGUL CLI · Linux 16.6 min 9 MB peak memory
SEGUL GUI · Linux 16.8 min 188 MB peak memory
Picking files one by one makes phones and tablets copy each file into the app first, which is slow for large batches. For more than about 500 files, use Add folder or Open archive (one .zip or .tar.gz file) instead. See file input .
Copyright © 2026 H. Handika & J. A. Esselstyn.
This material is based upon work supported by the National Science Foundation under grant numbers: DEB-1754393 and DEB-2244754. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.
