macOS
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brew install fastgaprovider-native install command
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Install fastga with Homebrew
Pairwise whole genome aligner. Version 1.5 via Homebrew; verified 2026-08-02.
install
Additional install commands
overview
Package summary
Pairwise whole genome aligner
Project links
Commands and aliases
- ALNchain
- ALNplot
- ALNreset
- ALNshow
- ALNtoPAF
- ALNtoPSL
- ANOshow
- ANOstat
- ANOtoBED
- BEDtoANO
- FAtoGDB
- FastGA
- FastKS
- GDBshow
- GDBstat
- GDBtoFA
- GIXcp
- GIXmake
- GIXmv
- GIXrm
- GIXshow
- ONEalnTEST
- ONEview
- PAFtoALN
- PAFtoPSL
history
Project history and usage
FASTGA is a pairwise whole-genome aligner by Gene Myers and Chenxi Zhou. It compares two genomes, or a genome against itself, and outputs alignments in formats such as `.1aln`, PAF, and PSL.
Project history
The FASTGA README identifies the authors, gives May 10, 2023 as the first date, and describes the tool as a fast genome aligner for high-quality, nearly complete genomes. Its design builds on adaptive seed finding and the wave-based local alignment approach associated with Myers' earlier DALIGNER work.
The package is more than one binary. It includes conversion, indexing, viewing, plotting, annotation, and file-management utilities around genome databases, genome indexes, ONEcode alignment files, PAF, PSL, BED, and ANO files.
The README's version notes show active development through 2025, including soft masking, log-file support for HPC cluster use, improved GIXmake memory behavior, faster conversion utilities, a ONEaln C library, and ANO annotation-file support.
Adoption history
FASTGA is niche scientific software rather than a general developer tool, but its official README includes Bioconda and Anaconda badges and Homebrew packages it as a formula. That places it in the practical bioinformatics packaging ecosystem where command-line tools are installed into reproducible analysis environments.
Its adoption case is strongest for users who already understand genome alignment workflows and want a performant aligner with reusable intermediate genome databases and indexes. The README emphasizes comparing large genomes quickly, keeping compact binary alignment outputs, and converting to common exchange formats when needed.
How it is used
Basic usage can be as simple as `FastGA A B` for two FASTA or ONEcode sequence inputs, streaming PAF output by default. The tool can also compare a genome against itself, keep persistent GDB and GIX intermediates, output PSL or binary ONEcode ALN files, and convert results with helper tools such as ALNtoPAF and ALNtoPSL.
FASTGA's workflow creates or reuses genome databases and genome indexes, then records alignments in a compact `.1aln` representation. Users handling repeated comparisons can prebuild GDB and GIX files to avoid repeated conversion and indexing costs.
Why package nerds care
FASTGA is package-nerd interesting because bioinformatics packages often ship a constellation of small command-line utilities rather than one executable. The Homebrew formula exposes a whole toolkit for converting, indexing, aligning, inspecting, plotting, and translating genome alignment data.
Its significance is also in file formats: GDB, GIX, `.1aln`, ONEcode, PAF, PSL, BED, and ANO support make it useful in pipelines where compact intermediate storage and standards-adjacent interchange formats both matter.
Timeline
- 2023: The README records May 10, 2023 as the first date for FASTGA.
- 2025: Version 1.3 added soft masking and log-file support.
- 2025: Version 1.4 added the ONEaln C library.
- 2025: Version 1.5 added ONEcode ANO-file support.
Related projects
- DALIGNER is cited by FASTGA as an earlier Myers aligner whose wave-based local aligner influenced FASTGA.
- ONEcode is used for FASTGA's genome database and alignment encodings.
- PAF and PSL are common output formats FASTGA can emit or convert to.
Sources
security posture
Risk level: green
narrow executable package without higher-risk signals.
Risk classifier
green risk · low confidence · appliance
Why
- narrow executable package without higher-risk signals
Signals
- metadata:no-higher-risk-signals
Install behavior
- No Homebrew bottle metadata was recorded.
Recommended review
Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.
executables
Installed executables
| Command | Kind | Exposure | Note |
|---|---|---|---|
ALNchain | executable | indexed executable | Discovered from the local executable index. |
ALNplot | executable | indexed executable | Discovered from the local executable index. |
ALNreset | executable | indexed executable | Discovered from the local executable index. |
ALNshow | executable | indexed executable | Discovered from the local executable index. |
ALNtoPAF | executable | indexed executable | Discovered from the local executable index. |
ALNtoPSL | executable | indexed executable | Discovered from the local executable index. |
ANOshow | executable | indexed executable | Discovered from the local executable index. |
ANOstat | executable | indexed executable | Discovered from the local executable index. |
ANOtoBED | executable | indexed executable | Discovered from the local executable index. |
BEDtoANO | executable | indexed executable | Discovered from the local executable index. |
FAtoGDB | executable | indexed executable | Discovered from the local executable index. |
FastGA | executable | indexed executable | Discovered from the local executable index. |
FastKS | executable | indexed executable | Discovered from the local executable index. |
GDBshow | executable | indexed executable | Discovered from the local executable index. |
GDBstat | executable | indexed executable | Discovered from the local executable index. |
GDBtoFA | executable | indexed executable | Discovered from the local executable index. |
GIXcp | executable | indexed executable | Discovered from the local executable index. |
GIXmake | executable | indexed executable | Discovered from the local executable index. |
GIXmv | executable | indexed executable | Discovered from the local executable index. |
GIXrm | executable | indexed executable | Discovered from the local executable index. |
GIXshow | executable | indexed executable | Discovered from the local executable index. |
ONEalnTEST | executable | indexed executable | Discovered from the local executable index. |
ONEview | executable | indexed executable | Discovered from the local executable index. |
PAFtoALN | executable | indexed executable | Discovered from the local executable index. |
PAFtoPSL | executable | indexed executable | Discovered from the local executable index. |
freshness
Version and freshness
These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.
page generated2026-08-03
manager version1.5
manager updated2026-08-02
local dataunknown
upstreamnot available
latest detectednot detected
- okNo freshness warnings were generated.
install metadata
Package metadata
| Package key | brew:fastga |
|---|---|
| Version | 1.5 |
| Package manager | Homebrew |
| Homepage | https://github.com/thegenemyers/FASTGA |
| Repository | https://github.com/thegenemyers/FASTGA |
| Last updated | 2026-08-02T16:35:31+09:00 |
| Pulse | updated |
| Bottle | not recorded |
| Service | none declared |
source trail
Generated from repository data
This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.
Combined YAML source
View the package source record on GitHub.
Used sources
- Geiger risk classifier
- Nucleus package database
- curated package history
- pkgdb category and tag curation