# 使用 Homebrew, apt, MacPorts, Nix 安装 veryfasttree 查看 veryfasttree 的安装路径、可执行文件、元数据以及面向 AI 代理工作流的安全说明。 ## 安装 ```sh sudo av install brew:veryfasttree ``` 其他安装命令: ### macOS - Homebrew (100%): ```sh brew install veryfasttree ``` 证据: local Homebrew formula metadata - MacPorts (94%): ```sh sudo port install veryfasttree ``` 证据: MacPorts ports tree: science/veryfasttree/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1 ### Linux - Debian apt (92%): ```sh sudo apt install veryfasttree ``` 证据: Debian stable package indexes: veryfasttree from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz - Nix (92%): ```sh nix profile install nixpkgs#veryfasttree ``` 证据: nixpkgs package indexes: pkgs/by-name/ve/veryfasttree/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 ## 软件包事实 - **软件包键:** brew:veryfasttree - **软件包管理器:** Homebrew - **软件包管理器页面:** - **版本:** 4.0.5 - **来源摘要:** Efficient phylogenetic tree inference for massive taxonomic datasets - **主页:** - **仓库:** - **上游文档:** - **许可证:** GPL-3.0-only AND BSD-3-Clause AND MPL-2.0 - **源码归档:** - **已生成:** 2026-07-08T18:08:21+00:00 ## 可执行文件 - VeryFastTree (cli) - VeryFastTree (别名) ## 依赖 - libomp ## 构建依赖 - boost - cmake - robin-map - xxhash ## macOS 提供的库 - bzip2 ## 安装行为 - post-install 钩子: 未定义 - Bottle: 可用 于 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## 版本和新鲜度 - 页面生成时间: 2026-07-08 - 管理器版本: 4.0.5 - 本地数据: OK - 上游仓库: https://github.com/citiususc/veryfasttree - 检测到的最新版本: v4.0.5 (当前) - 信息: No package-manager update timestamp was available. ## 项目历史与用法 VeryFastTree is a phylogenetic tree inference tool for very large sequence alignments. It is a tuned implementation of FastTree-2 that keeps the same broad methods and command-line interface while adding parallelization, vectorization, deterministic execution, and later memory-management improvements. ### 项目历史 The project began publicly in 2019 and was introduced in a 2020 Bioinformatics paper by researchers at CiTIUS, Universidade de Santiago de Compostela. The paper framed VeryFastTree as a response to FastTree-2's limited scalability: FastTree-2 was already a successful large-phylogeny tool, but important maximum-likelihood rearrangement and posterior-distribution steps did not scale well across threads. VeryFastTree v3.0 refactored and optimized the FastTree-2 code in C++ with OpenMP, added more complete vector-instruction support, parallelized major tree-improvement phases, and made same-thread-count parallel runs deterministic. The authors reported that a 330,000-sequence alignment could be processed in 4.5 hours on a standard server, substantially faster than FastTree-2 in their benchmark. Version 4.0, described in a 2024 GigaScience paper, pushed the same idea to million-taxon datasets. It parallelized more tree traversal operations, including subtree pruning and regrafting moves, added compressed and new file-format support, improved compatibility, and introduced disk-computing functionality for users without enough RAM for the largest jobs. ### 采用历史 The project deliberately preserved FastTree-2's command-line arguments so researchers could replace a FastTree-2 invocation with `VeryFastTree` and keep the same workflow. That compatibility is an important adoption mechanism in bioinformatics, where command lines are often embedded in scripts, notebooks, and pipeline definitions. The 2024 paper and project README point to research-community adoption by emphasizing availability, packaging in scientific software channels, and Python bindings. Its relevance grew with the scale of modern sequencing datasets, where tree-building for hundreds of thousands or millions of taxa is a practical bottleneck rather than an edge case. ### 使用方式 VeryFastTree is used to infer approximate maximum-likelihood phylogenies from nucleotide or protein alignments in formats such as FASTA, FASTQ, NEXUS, and PHYLIP. Users typically pass the same options they would pass to FastTree-2, adding VeryFastTree-specific controls when tuning thread count, deterministic mode, vector extensions, disk computing, or GPU-related experimental paths. Its package-nerd appeal is that it is a drop-in performance replacement rather than a new workflow to learn. In a field full of heavyweight scientific tools, keeping the old command surface while changing the performance envelope is a practical way to get into existing pipelines. ### 为什么软件包爱好者会关心 VeryFastTree matters because it turns a known scientific workhorse into something more suitable for current dataset sizes. It preserves the pragmatic FastTree-2 tradeoff of fast approximate maximum-likelihood inference, but makes that tradeoff viable on larger multicore servers and, with v4.0, on million-taxon alignments. ### 时间线 - 2019-12-02: GitHub repository created. - 2020-06-23: Bioinformatics paper published introducing VeryFastTree for large alignments. - 2020-06-25: v3.0 GitHub release published. - 2023-06: v4.0 release introduced new thread levels and broader parallelization. - 2024-08-08: GigaScience paper published describing VeryFastTree 4.0 and million-taxon benchmarks. ### Related projects - FastTree-2: the direct methodological and command-line ancestor. - RAxML, PhyML, and IQ-TREE: other maximum-likelihood phylogeny tools discussed in the Bioinformatics paper as part of the large-tree inference landscape. - VeryFastTree Python bindings: a related package for embedding the tool in Python workflows. ### 来源 - - - - - ## 安全说明 narrow executable package without higher-risk signals. - **Geiger 风险:** 绿色 / 低 - narrow executable package without higher-risk signals ## 源数据库详情 - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** veryfasttree - **Version Scheme:** 0 - **Revision:** 0 - **Head Version:** HEAD - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** head, stable ## 其他软件包管理器记录 - Debian apt - veryfasttree - 4.0.4+dfsg-2: normalized package name match | Debian stable package indexes: veryfasttree from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | Speeding up the estimation of phylogenetic trees from sequences | https://github.com/citiususc/veryfasttree - Nix - veryfasttree: normalized package name match | nixpkgs package indexes: pkgs/by-name/ve/veryfasttree/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Ubuntu apt - veryfasttree - 4.0.3+dfsg-1: normalized package name match | Ubuntu 24.04 LTS package indexes: veryfasttree from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | Speeding up the estimation of phylogenetic trees from sequences | https://github.com/citiususc/veryfasttree - MacPorts - veryfasttree: normalized package name match | MacPorts ports tree: science/veryfasttree/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1 ## 相关链接 - [Source-control packages](https://www.automicvault.com/zh-hans/pkg/source-control-tools/) - Belongs to a source-control command family. - [Terminal utility packages](https://www.automicvault.com/zh-hans/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://www.automicvault.com/zh-hans/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Scientific computing packages](https://www.automicvault.com/zh-hans/pkg/scientific-computing-tools/) - Matched scientific computing metadata. - [cmake](https://www.automicvault.com/zh-hans/pkg/brew/cmake/) - Build dependency declared by Homebrew. - [xxhash](https://www.automicvault.com/zh-hans/pkg/brew/xxhash/) - Build dependency declared by Homebrew. - [fastme](https://www.automicvault.com/zh-hans/pkg/brew/fastme/) - Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science. - [paml](https://www.automicvault.com/zh-hans/pkg/brew/paml/) - Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science. - [trimal](https://www.automicvault.com/zh-hans/pkg/brew/trimal/) - Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science. - [raxml-ng](https://www.automicvault.com/zh-hans/pkg/brew/raxml-ng/) - Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science, tree-inference. - [hyphy](https://www.automicvault.com/zh-hans/pkg/brew/hyphy/) - Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science. - [iqtree3](https://www.automicvault.com/zh-hans/pkg/brew/iqtree3/) - Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science. - [mrbayes](https://www.automicvault.com/zh-hans/pkg/brew/mrbayes/) - Shares av.db curated category or tags: bioinformatics, cli, phylogenetics, science. - [abpoa](https://www.automicvault.com/zh-hans/pkg/brew/abpoa/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [kraken2](https://www.automicvault.com/zh-hans/pkg/brew/kraken2/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, libomp, science, taxonomic. - [btllib](https://www.automicvault.com/zh-hans/pkg/brew/btllib/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, libomp, science. ## Combined YAML source View the package source record on GitHub. [combined/veryfasttree.yml](https://github.com/automic-vault/db/blob/main/combined/veryfasttree.yml) ## 来源 - Nucleus package database - Geiger risk classifier - package-page enrichment - curated package history - package version freshness - av.db category and tag curation - package relationship graph - external package-manager database matches - cross-ecosystem install command graph