SEGUL

An ultrafast and mobile-friendly phylogenomic toolkit.

Runs natively on the device you already have, from a phone to a computing cluster: iOS, Android, Windows, macOS, and Linux, on ARM and x86.

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SEGUL

From raw reads to alignment supermatrix

Prepare large phylogenomic datasets efficiently in one place

9 tools →

Alignments

Multi-locus alignment matrices

Concatenate Convert Compute genetic distances Filter Convert partition Split Summarize Trim Unalign
8 tools →

Sequences

Samples and IDs inside alignments

Add Extract Extract and map Filter Remove Rename Translate Transpose
4 tools →

Genomics

Raw reads and assemblies

Summarize reads Summarize contigs Convert MAF Summarize MAF
~/phylogenomics

# Concatenate 4,000 loci into a supermatrix

$ segul align concat -d loci/ --output supermatrix --part raxml

# Keep loci with at least 75% taxon coverage

$ segul align filter -d loci/ --percent 0.75

# Summarize raw reads

$ segul read summary -d raw_reads/

$

File formats

Support for various sequence formats.

  • FASTA

    Alignments, contigs

    .fasta .fa .fas

  • NEXUS

    Alignments

    .nex .nexus

  • PHYLIP

    Relaxed alignments

    .phy .phylip

  • FASTQ.gz

    Raw reads

    .fastq .fq

  • MAF.gz

    Genome alignments

    .maf

  • BED.gz

    Loci

    .bed

  • Partitions

    RAxML, NEXUS

    .txt .nex

All supported extensions →

Guided workflows

Common data summary, cleaning, and shaping tasks.

Build a phylogenomic supermatrix

  1. Summarize
  2. Filter
  3. Concatenate

Check a sequencing run

  1. Read summary
  2. Contig summary

Clean up sample names

  1. Extract IDs
  2. Rename

Reformat for another program

  1. Convert
  2. Partition

Easy to use

A guided graphical app and a concise command line, backed by documentation for every feature.

Accessible and reproducible

Runs on phones, laptops, and clusters with no runtime dependencies, Docker, or Singularity.

Fast and memory efficient

Written in Rust and parallel by default, making it simple to use, fast and memory efficient.

Interfaces

Different ways to interact with SEGUI.

GUI

SEGUI app

Point-and-click tools for desktop, tablet, and phone. Install from your platform's app store.

Installation guide →

CLI

Command line

Script thousands of loci in a pipeline. Install from Bioconda, cargo, or a pre-built binary.

$ conda install bioconda::segul
Installation guide →

API

Python, Rust, and R

Call SEGUL from your own code with pysegul or the segul crate.

$ pip install pysegul
Installation guide →

Install SEGUI, free.

Desktop, tablet, and phone. Looking for the command line? See every install option.

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

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