此列表收集了比较基因组相关的工具。
- [ANI calculator] - [web]
- [AAI calculator] - [web]
- [fastANI] - [C++, v1.34, 2023.07] - [2018.11, Nat Comm] - [High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries.]
- [SVbyEye] - [R, active dev, No tag] - [2024.09, bioRxiv] - [SVbyEye: A visual tool to characterize structural variation among whole genome assemblies.]
- [CompareM] - [Python, v0.1.2, 2020.12] - [Unsupported. Lasted version Dec 31 2020.]
- [EzAAI] - [Java, v1.2.3, 2024.02] - [2021.04, J Microbiol] - [Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity.]
- [SynTracker] - [Python, v1.3.1, 2024.09 ] - [2024.06, Nat Biotechnol] - [Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution.]
- [skani] - [Rust, v0.2.2, 2024.07] - [2023.09, Nat Methods] - [Fast and robust metagenomic sequence comparison through sparse chaining with skani]
- ANIclustermap - [Python, v1.4.0, 2024.7] - [Shimoyama, Y. (2022). ANIclustermap: A tool for drawing ANI clustermap between all-vs-all microbial genomes [Computer software].]
- [SCARAP] - [Python, v1.0.0, 2024.11] - [2024.12, Bioinformatics] - [SCARAP: scalable cross-species comparative genomics of prokaryotes]
- [gggenes] - [Draw gene arrow maps in ggplot2]
- [LoVis4u] - [Python, v0.0.11, 2024.10] - [2024.9, bioRxiv] - [LoVis4u: Locus Visualisation tool for comparative genomics.]
- [gggenomes] - [gggenomes: A Grammar of Graphics for Comparative Genomics]
- [plasmapR] - [Creating plasmid maps inside ggplot.]
- WAFFLE - [Python, v1.1.0, 2024.10] - [2025.1, Nat Microbiol] - [Profiling lateral gene transfer events in the human microbiome using WAAFLE.]