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Install fastme with Homebrew

Accurate and fast distance-based phylogeny inference program. Version 2.1.6.3 via Homebrew; verified from local package data.

Install commandSecurity notes

install

Additional install commands

macOS

Homebrewverified · 100%
brew install fastme

local Homebrew formula metadata

overview

Package summary

Accurate and fast distance-based phylogeny inference program

Commands and aliases

  • fastme

history

Project history and usage

FastME is a distance-based phylogeny inference program from the ATGC/LIRMM ecosystem. It focuses on balanced minimum evolution methods and exposes both command-line and web-application use.

Project history

FastME traces back to the 2002 minimum-evolution phylogeny reconstruction work by Desper and Gascuel. The ATGC project page describes the original FastME as using nearest-neighbor interchange and the 2.0 line as adding subtree pruning and regrafting while remaining fast enough to compare with neighbor joining.

The 2015 FastME 2.0 publication and ATGC page frame the modern package as a comprehensive distance-method toolkit, adding distance estimation for DNA and protein data, bootstrapping, and parallel computations.

Adoption history

FastME is a specialist phylogenetics tool rather than a broad developer utility. Its adoption surface is the ATGC web service, Linux and Mac command-line binaries, Galaxy integration references, and scientific package-manager distribution.

How it is used

Users run FastME to infer phylogenetic trees from sequence-derived distances when they want a fast distance method with topology-improvement steps beyond plain neighbor joining. The project does not document a persistent user configuration or credentials file.

Why package nerds care

For package maintainers, FastME is the classic scientific CLI shape: an academic algorithm with a paper trail, an official web runner, and a small native command-line binary that needs to stay reproducible across Unix-like systems.

Timeline

  • 2002: Minimum-evolution algorithms underlying FastME are published.
  • 2015: FastME 2.0 paper describes the expanded NNI and SPR implementation.
  • 2016: ATGC metadata lists the FastME software page as published.
  • 2017: The official LIRMM GitLab project is created.

Related projects

  • FastME is related to neighbor joining and other distance-based phylogeny tools; its own documentation emphasizes balanced minimum evolution, NNI, and SPR.

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 post-install hook is recorded in formula metadata.
  • Homebrew bottle metadata is available for 10 platform targets.
  • Installs with 1 runtime dependencies.

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

CommandKindExposureNote
fastmecliglobal executable

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 generated2026-07-08
manager version2.1.6.3
manager updated
local dataok
upstreamnot checked
latest detectednot detected

http://www.atgc-montpellier.fr/fastme/

  • infoNo package-manager update timestamp was available.low confidence
  • infoRelease/tag comparison is only available for GitHub repositories.http://www.atgc-montpellier.fr/fastme/none confidence

install metadata

Package metadata

Package keybrew:fastme
Version2.1.6.3
Package managerHomebrew
Package manager pagehttps://formulae.brew.sh/formula/fastme
Homepagehttp://www.atgc-montpellier.fr/fastme/
Repositoryhttps://gite.lirmm.fr/atgc/FastME
Upstream docshttp://www.atgc-montpellier.fr/fastme
LicenseGPL-3.0-or-later
Source archivehttps://gite.lirmm.fr/atgc/FastME/raw/v2.1.6.3/tarball/fastme-2.1.6.3.tar.gz
Dependencieslibomp
Bottleavailable (on arm64_linux, arm64_monterey, arm64_sequoia, arm64_sonoma, arm64_tahoe, arm64_ventura, monterey, sonoma, ventura, x86_64_linux)
Homebrew post-installnot defined
Servicenone declared

registry facts

Source database details

Source DatabaseHomebrew formula API
Taphomebrew/core
Full Namefastme
Version Scheme0
Revision1
Bottle Stable Root URLhttps://ghcr.io/v2/homebrew/core
Deprecatedno
Disabledno
Keg Onlyno
URL Keys
  • stable

package graph

Links come from deterministic package relationships, av.db category and tag curation, ecosystem matches, and package hub membership.

Related tools

Same workflow

  • pamlShares av.db curated category or tags: bioinformatics, cli, phylogenetics, science.
  • trimalShares av.db curated category or tags: bioinformatics, cli, phylogenetics, science.
  • veryfasttreeShares av.db curated category or tags: bioinformatics, cli, phylogenetics, science.
  • hyphyShares av.db curated category or tags: bioinformatics, cli, phylogenetics, science.
  • iqtree3Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science.
  • mrbayesShares av.db curated category or tags: bioinformatics, cli, phylogenetics, science.

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.

Used sources

  • Geiger risk classifier
  • Nucleus package database
  • av.db category and tag curation
  • cross-ecosystem install command graph
  • curated package history
  • package relationship graph
  • package version freshness
  • package-page enrichment