Quick Start

SEGUL comes as a desktop and mobile app (GUI), a terminal command (CLI), and libraries for Python, Rust, and R (API). This page gets you from install to a first run.

1. Choose an interface

Not sure? Install both. The GUI and CLI do not interfere with each other.

See CLI vs GUI for platforms, feature differences, and benchmarks.

2. Install

GUI

Install SEGUI, the SEGUL app, from your platform's store. See the GUI installation guide for requirements and other options.

Get it fromMicrosoft StoreDownload on theApp StoreGet it onGoogle PlayGet it from theSnap Store

CLI

On Linux and macOS, the installer script picks the right build and needs no root access:

curl -fsSL https://segul.app/install.sh | sh

On Windows, or to install by hand, download the binary for your system, unpack it, and put segul on your PATH. The CLI installation guide walks through each method.

Linux

• x86_64Modern distributions and WSL↓
• x86_64 staticOlder GLIBC, common on HPC↓
• ARM64ARM servers and boards↓

macOS

• Apple siliconM-series Macs↓
• IntelIntel Macs↓

Windows

• x86_64Most Windows PCs↓
• ARM64Windows on ARM, Copilot+ PCs↓

On Linux or macOS with Bioconda set up, you can use conda instead. It may not work on older Linux systems found on some HPC clusters. See the Bioconda guide.

conda install bioconda::segul

Python

PySEGUL is the Python binding to the SEGUL library. It needs no Rust knowledge.

pip install pysegul

Rust

Add the SEGUL crate from crates.io to your project. The same crate also works from R, which needs some Rust knowledge.

cargo add segul

3. Run your first task

Try SEGUL with a small example dataset, then move on to your own data.

NEXUS alignmentsdata-nexus.zip

FASTA alignmentsdata-fasta.zip

Relaxed PHYLIP alignmentsdata-phylip.zip, sequential and interleaved

Concatenated NEXUSdata-concat-nex.zip, for splitting

Genomic files are too large to bundle. Download reads or contigs from public repositories such as NCBI SRA.

GUI

Removing an input file only takes it off the list. It stays on disk.

1. Open the app and choose a task group in the navigation bar, such as Alignments. Then pick a tool, such as Concatenate alignments. On narrow windows, tap the tool name at the top to switch tools.
2. Select Browse files, Browse folder, or Open archive to add the input.
3. Choose an output folder and fill in any parameters the task needs. On mobile, output goes to the app's own folder.
4. Select Run. Open the output files in the built-in viewer, or export them as a ZIP or gzip archive.

Caution

Phones and tablets copy each picked file into the app first. For large datasets, use Add folder or Open archive instead. See file input.

CLI

Without --output, SEGUL writes to a default folder named after the task, such as Align-Concat.

SEGUL detects the input format from the file extension. For other extensions, set it with --input-format. Common commands:

segul align concat -d alignments/   # Concatenate alignments
segul align convert -d alignments/  # Convert alignment formats
segul align summary -d alignments/  # Alignment summary statistics
segul sequence remove -d alignments/ --id="seq_1;seq_2" # Remove sequences
segul read summary -d reads/        # Read summary statistics
segul <command> <subcommand> --help # Options for any task

See the command options for every flag.

Note

SEGUL 0.19.0 introduced the command subcommand layout. Older versions use a single command and need an input format with a folder, such as segul concat -d alignments/ -f nexus.

Python

Concatenate a folder of NEXUS alignments into FASTA with a RAxML partition file:

import pysegul

concat = pysegul.AlignmentConcatenation(
    "nexus",          # input format
    "dna",            # data type
    "output",         # output folder
    "fasta",          # output format
    "raxml",          # partition format
    "concatenated",   # output file prefix
)
concat.from_dir("alignments")

Most classes follow this pattern. Tasks with extra parameters, such as filtering or extraction, set the input first and then call a method. See the PySEGUL guide.

Rust

See the Rust API guide and the crate documentation.

4. Explore the tools

SEGUL groups its tools by the kind of input they take:

Each task group is a button in the GUI navigation and a command group in the CLI.

It reads these file formats:

Compressed files end in .gz. SEGUL reads them directly, without decompressing them first.

Tip

The CLI also accepts non-standard extensions with --input-format. The GUI only lists supported extensions, so rename such files first.

FeaturesWhat each tool does, with diagrams

GUI usageStep-by-step guides for the app

CLI usageCommands and options

API usagePython, Rust, and R