Science Score: 67.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 4 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
1 of 4 committers (25.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.6%) to scientific vocabulary
Keywords
Repository
An ultrafast and memory efficient tool for phylogenomics
Basic Info
- Host: GitHub
- Owner: hhandika
- License: mit
- Language: Rust
- Default Branch: main
- Homepage: https://segul.app
- Size: 1.86 MB
Statistics
- Stars: 26
- Watchers: 2
- Forks: 2
- Open Issues: 0
- Releases: 66
Topics
Metadata Files
README.md
SEGUL 
SEGUL simplifies complex, tedious, and error-prone data wrangling and summarization for genomics and Sanger datasets. We develop it to be easy for beginners while providing advanced features for experienced users. SEGUL is also a high performance and memory efficient genomic tool. In our tests, it consistently offers a faster and more efficient (low memory footprint) alternative to existing applications for various genomic tasks (see benchmark).
SEGUL runs on many software platforms, from mobile devices and personal computers to high-performance computing clusters. It is available as a command-line interface (CLI), a graphical user interface (GUI) application, and a Rust library and Python package (see platform support below). SEGUL is part of our ongoing effort to ensure that genomic software is accessible to everyone, regardless of their bioinformatic skills and computing resources.
Learn more about SEGUL in the documentation. We welcome feedback if you find any issues, difficulties or have ideas to improve the app and its documentation (details below).
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.
Essential Links
- App Documentation: EN
- API Documentation: Rust • Python
- GUI: Source code • Installation • App Store • Google Play • Snap Store • Microsoft Store
- CLI: Downloads • Docs
- Bioconda (CLI): Package • Docs
- Python package: Source code • PyPI • Docs
Supported File Formats
Sequence formats:
- NEXUS
- Relaxed PHYLIP
- FASTA
- FASTQ (gzipped and uncompressed)
- Multiple Alignment Format (MAF) (In development)
- Variant Call Format (VCF) (In development)
All formats are supported in interleave and sequential versions. The app supports DNA and amino acid sequences, except for FASTQ, MAF, and VCF (DNA only).
Alignment partition formats:
- RaXML
- NEXUS
The NEXUS partition can be written as a charset block embedded in NEXUS formatted sequences or a separate file.
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]
- Bioconda: [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:
bash
cargo add segul
Python
We provide binding for Python (called pysegul). Use SEGUL just like any other Python package:
python
pip install pysegul
Learn more about using SEGUL API in the documentation.
Features
NOTES: To try beta features, follow the installation instruction for the beta version.
| Features | Supported Input Formats | Guideline Quick Links | | ------------------------------ | ----------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | Alignment concatenation | FASTA, NEXUS, PHYLIP | CLI / GUI / Python | | Alignment conversion | FASTA, NEXUS, PHYLIP | CLI / GUI / Python | | Alignment filtering | FASTA, NEXUS, PHYLIP | CLI / GUI / Python | | Alignment splitting | FASTA, NEXUS, PHYLIP | CLI / GUI / Python | | Alignment partition conversion | RaXML, NEXUS | CLI / GUI / Python | | Alignment summary statistics | FASTA, NEXUS, PHYLIP | CLI / GUI / Python | | Alignment trimming | FASTA, NEXUS, PHYLIP | CLI (Beta) / Coming soon | | Genomic summary statistics | FASTQ, FASTA (contigs) | CLI / GUI / Python | | Multiple alignment conversion | MAF | CLI (Beta) / Coming soon | | Sequence addition | FASTA, NEXUS, PHYLIP | CLI (Beta) / Coming soon | | Sequence extraction | FASTA, NEXUS, PHYLIP | CLI / GUI / Python | | Sequence filtering | FASTA, NEXUS, PHYLIP | CLI / Coming soon | | Sequence ID extraction | FASTA, NEXUS, PHYLIP | CLI / GUI / Python | | Sequence ID mapping | FASTA, NEXUS, PHYLIP | CLI / GUI / Python | | Sequence ID renaming | FASTA, NEXUS, PHYLIP | CLI / GUI / Coming soon | | Sequence removal | FASTA, NEXUS, PHYLIP | CLI / GUI / Python | | Sequence translation | FASTA, NEXUS, PHYLIP | CLI / GUI / Python |
Contribution
We welcome any contribution, from issue reporting and ideas to improve the app and documentation to code contribution. For ideas and issue reporting, please post on the Github issues page. For code contribution, please fork the repository and send pull requests to this repository.
Owner
- Name: Heru Handika
- Login: hhandika
- Kind: user
- Location: Baton Rouge, USA
- Website: https://hhandika.com/
- Twitter: heru_hdk
- Repositories: 16
- Profile: https://github.com/hhandika
A daily field biologist and taxonomist && nightly programmer.
Citation (CITATION.cff)
cff-version: 1.2.0
message: Please cite the following works when using this software.
preferred-citation:
abstract: >-
<jats:title>Abstract</jats:title><jats:p>Phylogenetic studies now routinely
require manipulating and summarizing thousands of data files. For most of
these tasks, currently available software requires considerable computing
resources and substantial knowledge of command‐line applications. We develop
an ultrafast and memory‐efficient software, SEGUL, that performs common
phylogenomic dataset manipulations and calculates statistics summarizing
essential data features. Our software is available as standalone
command‐line interface (CLI) and graphical user interface (GUI)
applications, and as a library for Rust, R and Python, with possible support
of other languages. The CLI and library versions run native on Windows,
Linux and macOS, including Apple ARM Macs. The GUI version extends support
to include mobile iOS, iPadOS and Android operating systems. SEGUL leverages
the high performance of the Rust programming language to offer fast
execution times and low memory footprints regardless of dataset size and
platform choice. The inclusion of a GUI minimizes bioinformatics barriers to
phylogenomics while SEGUL's efficiency reduces economic barriers by allowing
analysis on inexpensive hardware. Our support for mobile operating systems
further enables teaching phylogenomics where access to computing power is
limited.</jats:p>
authors:
- family-names: Handika
given-names: Heru
- family-names: Esselstyn
given-names: Jacob A.
doi: 10.1111/1755-0998.13964
identifiers:
- type: doi
value: 10.1111/1755-0998.13964
- type: url
value: http://dx.doi.org/10.1111/1755-0998.13964
- type: other
value: urn:issn:1755-098X
title: >-
SEGUL: Ultrafast, memory‐efficient and mobile‐friendly software for
manipulating and summarizing phylogenomic datasets
url: http://dx.doi.org/10.1111/1755-0998.13964
database: Crossref
date-published: 2024-04-26
year: 2024
month: 4
issn: 1755-098X
journal: Molecular Ecology Resources
languages:
- en
publisher:
name: Wiley
type: article
GitHub Events
Total
- Watch event: 3
- Push event: 40
Last Year
- Watch event: 3
- Push event: 40
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Heru Handika | h****g@g****m | 1,398 |
| Jake Esselstyn | e****n@l****u | 4 |
| Heru Handika | 4****a | 2 |
| Heru Handika | h****a@H****l | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 4
- Total pull requests: 0
- Average time to close issues: about 1 month
- Average time to close pull requests: N/A
- Total issue authors: 3
- Total pull request authors: 0
- Average comments per issue: 2.25
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: about 15 hours
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 4.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- stiatragul (2)
- hhandika (1)
- AntonioBaeza (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- cargo 67,420 total
- Total dependent packages: 1
- Total dependent repositories: 0
- Total versions: 61
- Total maintainers: 1
crates.io: segul
An ultrafast and memory-efficient tool for phylogenomics
- Homepage: https://www.segul.app/
- Documentation: https://docs.rs/segul/
- License: MIT
-
Latest release: 0.22.1
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
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