使用 Homebrew 安装 fastme

项目链接

• 主页

命令和别名

• fastme

项目历史

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.

采用历史

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.

使用方式

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.

为什么软件包爱好者会关心

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.

时间线

• 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.

来源

• http://www.atgc-montpellier.fr/fastme/
• https://gite.lirmm.fr/atgc/FastME
• https://doi.org/10.1093/molbev/msv150
• https://doi.org/10.1089/106652702761034136