数字农科院2.0

Kssdtree: an interactive Python package for phylogenetic analysis based on sketching technique

文献类型： 外文期刊

作者： Hang Yang;Xiaoxin Lu;Jiaxing Chang;Qing Chang;Wen Zheng;Zehua Chen;Huiguang Yi

作者机构：

关键词： （1-1-2）

期刊名称： Bioinformatics (Oxford, England)

ISSN： 1367-4811

年卷期： 2024 年 40 卷 10 期

页码：

收录情况： SCIE（2024版）

摘要： SUMMARY: Sketching technologies have recently emerged as a promising solution for real-time, large-scale phylogenetic analysis. However, existing sketching-based phylogenetic tools exhibit drawbacks, including platform restrictions, deficiencies in tree visualization, and inherent distance estimation bias. These limitations collectively impede the overall convenience and efficiency of the analysis. In this study, we introduce Kssdtree, an interactive Python package designed to address these challenges. Kssdtree surpasses other sketching-based tools by demonstrating superior performance in terms of both accuracy and time efficiency on comprehensive benchmarking datasets. Notably, Kssdtree offers key advantages such as intra-species phylogenomic analysis and GTDB-based phylogenetic placement analysis, significantly enhancing the scope and depth of phylogenetic investigations. Through extensive evaluations and comparisons, Kssdtree stands out as an efficient and versatile method for real-time, large-scale phylogenetic analysis. AVAILABILITY AND IMPLEMENTATION: The Kssdtree Python package is freely accessible at https://pypi.org/project/kssdtree and source code is available at https://github.com/yhlink/kssdtree. The documentation and instantiation for the software is available at https://kssdtree.readthedocs.io/en/latest. The video tutorial is available at https://youtu.be/_6hg59Yn-Ws.

分类号：

  • 相关文献

[1]强化无性繁殖作物育种基础研究 保障国家粮食和重要农产品稳定安全供给. 黄三文. 2024

[2]Recognition and Localization of Maize Leaf and Stalk Trajectories in RGB Images Based on Point-Line Net. Bingwen Liu,Jianye Chang,Dengfeng Hou,Yuchen Pan,Dengao Li,Jue Ruan. 2024

[3]Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes. Zeng, Xiaofei,Yi, Zili,Zhang, Xingtan,Du, Yuhui,Li, Yu,Zhou, Zhiqing,Chen, Sijie,Zhao, Huijie,Yang, Sai,Wang, Yibin,Chen, Guoan. 2024

[4]MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction. Fang Wang,Yibin Wang,Xiaofei Zeng,Shengcheng Zhang,Jiaxin Yu,Dongxi Li,Xingtan Zhang. 2024

[5]A soybean cyst nematode suppresses microbial plant symbionts using a lipochitooligosaccharide-hydrolysing enzyme. Chen, Wei,Wang, Di,Ke, Shaoyong,Cao, Yangrong,Xiang, Wensheng,Guo, Xiaoli,Yang, Qing. 2024

[6]A telomere-to-telomere genome assembly of cotton provides insights into centromere evolution and short-season adaptation. Hu, Guanjing,Wang, Zhenyu,Tian, Zunzhe,Wang, Kai,Ji, Gaoxiang,Wang, Xingxing,Zhang, Xianliang,Yang, Zhaoen,Liu, Xuan,Niu, Ruoyu,Zhu, De,Zhang, Yuzhi,Duan, Lian,Ma, Xueyuan,Xiong, Xianpeng,Kong, Jiali,Zhao, Xianjia,Zhang, Ya,Zhao, Junjie,He, Shoupu,Grover, Corrinne E.,Su, Junji,Feng, Keyun,Yu, Guangrun,Han, Jinlei,Zang, Xinshan,Wu, Zhiqiang,Pan, Weihua,Wendel, Jonathan F.,Ma, Xiongfeng. 2025

[7]Efficient data filtering with multiple group conditions: a command tool for bioinformatics data analysis. Wenpeng Deng, Jianye Chang,Alun Li,He Xie, Jue Ruan. 2025

[8]International research initiative on genomics-guided sugarcane breeding. Xingtan Zhang,Jungang Wang,Noor-ul-Áin,Youxiong Que,Jisen Zhang,Javeria Abid,Peifang Zhao,Yuebin Zhang,Jishan Lin,Li yu Chen,Yixue Bao,Robert Herry,Sithichoke Tangphatsornruang,Qinnan Wang,Dongliang Huang,Jian Ye,Muqing Zhang,Ming Luo,Mike Butterfield,Ren Wang,Ray Ming. 2025

[9]Leaf rolling detection in maize under complex environments using an improved deep learning method. Yuanhao Wang. 2024

[10]TSTA: Thread and SIMD-based trapezoidal pairwise/multiple sequence-Alignment method. Peiyu Zong,Wenpeng Den,Jian Liu,Jue Ruan. 2024

[11]Oxidative burst causes loss of tapetal Ubisch body and male sterility in rice. Chuanlin Shi,Shaohua Yang,Yan Cui,Zhan Xu,Bin Zhang,Mingliang Guo,Yiwang Zhu,Ying Yang,Feng Wang,Huaqing Liu,Yu Zhang,Qian Qian,Lianguang Shang. 2024

[12]Detection of fungal disease in citrus fruit based on hyperspectral imaging. 万方浩. 2025

[13]Post-translational modifications of SOG1 enable dynamic control of plant DNA damage response. Weiyi Bao,Zhiping Deng,Siyu Zhuang,Chenming Xu,Ziqian Yang,Mingxi Zheng,Ran Zhang,Meizhi Xu,Shunping Yan,Lili Wang. 2025

作者其他论文 更多>>