SEGUL

SEGUL is an ultra-fast, memory-efficient application for working with phylogenomic datasets. It is available as standalone, zero dependency command line, GUI applications (called SEGUI), and library/packages for Rust and other programming languages. It runs from your smartphone to High Performance Computers (see platform support below). It is safe, multi threaded, and easy to use.

It is designed to handle operations on large genomic datasets, while using minimal computational resources. However, it also provides convenient features for working on smaller datasets (e.g., Sanger datasets). In our tests, it consistently offers a faster and more efficient (low memory footprint) alternative to existing applications for a variety of sequence alignment manipulations (see benchmark).

Learn more about SEGUL in the documentation.

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. https://doi.org/10.1111/1755-0998.13964.

Installation

GUI Version

Desktop

Mobile

Learn more about device requirements and GUI app installation in the documentation.

CLI Version

The CLI app may work in any Rust supported platform. However, we only tested and officially support the following platforms:

Linux
MacOS
Windows
Windows Subsystem for Linux (WSL)

CLI Installation Methods

Pre-compiled binaries: [Releases] [Docs]
Conda: [Package] [Docs]
Package manager: [Docs]
From source: [Docs]
Beta version: [Docs]

API version

The API version is available for Rust and other programming languages. For Rust users, you can install it via Cargo:

cargo add segul

Python

We provide binding for Python (called pysegul). Use SEGUL just like any other Python package:

pip install pysegul

Learn more about using SEGUL API in the documentation.

Features

Feature	Quick Link
Alignment concatenation	CLI / GUI
Alignment conversion	CLI / GUI
Alignment filtering	CLI / GUI
Alignment splitting	CLI / GUI
Alignment partition conversion	CLI / GUI
Alignment summary statistics	CLI / GUI
Genomic summary statistics	CLI / GUI
Sequence extraction	CLI / GUI
Sequence filtering	CLI / GUI in development
Sequence ID extraction	CLI / GUI
Sequence ID mapping	CLI / GUI
Sequence ID renaming	CLI / GUI
Sequence removal	CLI / GUI
Sequence translation	CLI / GUI

Supported sequence formats:

NEXUS
Relaxed PHYLIP
FASTA
FASTQ (gzipped and uncompressed)

All of the formats are supported in interleave and sequential versions. Except for FASTQ (DNA only), the app supports both DNA and amino acid sequences.

Supported partition formats:

RaXML
NEXUS

The NEXUS partition can be written as a charset block embedded in NEXUS formatted sequences or a separate file.

Contribution

We welcome any kind of contribution, from issue reporting, ideas to improve the app, to code contribution. For ideas and issue reporting please post in the Github issues page. For code contribution, please fork the repository and send pull requests to this repository.

hhandika/segul