EasyCGTree:基于核心基因组的 prokaryotic 基因组分析的管道
Dao-Feng Zhang1, Wei He2, Zongze Shao3,4
1Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization and College of Oceanography, Hohai University, Nanjing, 210098, China. zdf@hhu.edu.cn.
BMC bioinformatics
|October 14, 2023
概括
简易CGTree简化了基因组规模的家族遗传树重建,用于缺乏生物信息学专业知识的研究人员. 这种用户友好型的管道提供了与现有方法可比的准确结果,使得族系学更容易获得.
科学领域:
- 微生物学 微生物学
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
背景情况:
- 基因组规模的遗传学分析至关重要,但对于非专家来说往往是复杂的.
- 目前用于重建家族遗传树的方法可能具有挑战性.
研究的目的:
- 介绍EasyCGTree,一个用户友好的,跨平台的管道,用于基因组规模的基因树重建.
- 为超矩阵 (SM) 和超树 (ST) 遗传学方法提供可访问的工具.
主要方法:
- EasyCGTree使用了Perl和预编译的知名程序,以方便安装和使用.
- 它结合了隐藏的马尔科夫模型 (HMMs),用于核心基因组的同类搜索.
- 该管道在43个Paracoccus基因组上进行了测试,将SM树与其他管道 (UBCG,bcgTree) 进行了比较.
主要成果:
- EasyCGTree成功地推断出共识,SM和ST树.
- 与参考管道相比,推断的SM树显示出高的拓相似性 (距离<0.1) 和精度 (CCC>0.99).
- 该管道在遗传树构建中的准确性和效率得到了验证.
结论:
- EasyCGTree提供了一个准确的,全合一的解决方案,用于族谱树的生成,简化安装和使用.
- 综合性ST方法提供了一个关于 prokaryotic 进化信号的新观点.
- 版本4免费提供给Linux和Windows用户.
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