使用 Homebrew, apt, Nix 安装 kalign

项目链接

• 主页

命令和别名

• kalign

项目历史

Timo Lassmann and Erik Sonnhammer published the original Kalign method in BMC Bioinformatics on 2005-12-12. The paper described a Wu-Manber-based progressive alignment method intended to improve both speed and accuracy for large comparative-genomics workloads.

采用历史

Kalign remained in the bioinformatics toolchain because multiple sequence alignment is a routine upstream step for homology, conserved-motif, phylogeny, and structure-oriented analyses. Kalign 3, published in Bioinformatics in 2019, was presented as a complete rewrite to handle larger protein and nucleotide sequence sets, using SIMD-accelerated distance estimation and fast guide-tree construction.

使用方式

Users run kalign on FASTA-like biological sequence inputs to produce multiple alignments. The modern README describes progressive alignment with multi-threading support, source builds with CMake, and alternatives such as Zig builds and Python packaging.

为什么软件包爱好者会关心

Kalign is a classic science CLI package: a published algorithm wrapped in a small executable, useful in scripts and pipelines, with package-manager availability making a cited method reproducible without hand-building a lab-specific binary.

时间线

• 2005-12-12: Original Kalign paper published in BMC Bioinformatics.
• 2019-10-26: Kalign 3 paper published in Bioinformatics.
• 2019-10-28: GitHub release 3.1 published.
• 2020-11-06: v3.3 release added multi-threading.
• 2026-02-27: Kalign 3.5.1 published.

Related projects

• Related multiple-sequence-alignment tools include ClustalW, MAFFT, MUSCLE, T-Coffee, and other progressive or consistency-based MSA programs.

来源

• https://academic.oup.com/bioinformatics/article/36/6/1928/5607735
• https://api.github.com/repos/TimoLassmann/kalign/releases?per_page=100
• https://github.com/TimoLassmann/kalign
• https://link.springer.com/article/10.1186/1471-2105-6-298