Ksak: A high-throughput tool for alignment-free phylogenetics
Phylogenetic tools are fundamental to the studies of evolutionary relationships. In this paper, we present Ksak, a novel high-throughput tool for alignment-free phylogenetic analysis. Ksak computes the pairwise distance matrix between molecular sequences, using seven widely accepted k-mer based dist...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2023-03-01
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| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1050130/full |
| _version_ | 1797829739850760192 |
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| author | Xuemei Liu Ziqi Cheng Guohao Xu Jiemin Xie Xudong Liu Bozhen Ren Dongmei Ai Yangxin Chen Yangxin Chen Li Charlie Xia |
| author_facet | Xuemei Liu Ziqi Cheng Guohao Xu Jiemin Xie Xudong Liu Bozhen Ren Dongmei Ai Yangxin Chen Yangxin Chen Li Charlie Xia |
| author_sort | Xuemei Liu |
| collection | DOAJ |
| description | Phylogenetic tools are fundamental to the studies of evolutionary relationships. In this paper, we present Ksak, a novel high-throughput tool for alignment-free phylogenetic analysis. Ksak computes the pairwise distance matrix between molecular sequences, using seven widely accepted k-mer based distance measures. Based on the distance matrix, Ksak constructs the phylogenetic tree with standard algorithms. When benchmarked with a golden standard 16S rRNA dataset, Ksak was found to be the most accurate tool among all five tools compared and was 19% more accurate than ClustalW2, a high-accuracy multiple sequence aligner. Above all, Ksak was tens to hundreds of times faster than ClustalW2, which helps eliminate the computation limit currently encountered in large-scale multiple sequence alignment. Ksak is freely available at https://github.com/labxscut/ksak. |
| first_indexed | 2024-04-09T13:26:06Z |
| format | Article |
| id | doaj.art-2b4bda122c0a448da62b4e0b7a2392fd |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-09T13:26:06Z |
| publishDate | 2023-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-2b4bda122c0a448da62b4e0b7a2392fd2023-05-10T10:32:25ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-03-011410.3389/fmicb.2023.10501301050130Ksak: A high-throughput tool for alignment-free phylogeneticsXuemei Liu0Ziqi Cheng1Guohao Xu2Jiemin Xie3Xudong Liu4Bozhen Ren5Dongmei Ai6Yangxin Chen7Yangxin Chen8Li Charlie Xia9School of Physics and Optoelectronics, South China University of Technology, Guangzhou, Guangdong, ChinaGuangzhou Boguan Telecommunication Technology Limited, Guangzhou, Guangdong, ChinaSchool of Mathematics, South China University of Technology, Guangzhou, Guangdong, ChinaSchool of Mathematics, South China University of Technology, Guangzhou, Guangdong, ChinaSchool of Physics and Optoelectronics, South China University of Technology, Guangzhou, Guangdong, ChinaSchool of Mathematics, South China University of Technology, Guangzhou, Guangdong, ChinaSchool of Mathematics and Physics, University of Science and Technology Beijing, Beijing, ChinaDepartment of Cardiology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, Guangdong, ChinaGuangzhou Key Laboratory of Molecular Mechanism and Translation in Major Cardiovascular Disease, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, ChinaSchool of Mathematics, South China University of Technology, Guangzhou, Guangdong, ChinaPhylogenetic tools are fundamental to the studies of evolutionary relationships. In this paper, we present Ksak, a novel high-throughput tool for alignment-free phylogenetic analysis. Ksak computes the pairwise distance matrix between molecular sequences, using seven widely accepted k-mer based distance measures. Based on the distance matrix, Ksak constructs the phylogenetic tree with standard algorithms. When benchmarked with a golden standard 16S rRNA dataset, Ksak was found to be the most accurate tool among all five tools compared and was 19% more accurate than ClustalW2, a high-accuracy multiple sequence aligner. Above all, Ksak was tens to hundreds of times faster than ClustalW2, which helps eliminate the computation limit currently encountered in large-scale multiple sequence alignment. Ksak is freely available at https://github.com/labxscut/ksak.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1050130/fullk-merphylogentic treealignment freeopen sourcemicrobiome |
| spellingShingle | Xuemei Liu Ziqi Cheng Guohao Xu Jiemin Xie Xudong Liu Bozhen Ren Dongmei Ai Yangxin Chen Yangxin Chen Li Charlie Xia Ksak: A high-throughput tool for alignment-free phylogenetics Frontiers in Microbiology k-mer phylogentic tree alignment free open source microbiome |
| title | Ksak: A high-throughput tool for alignment-free phylogenetics |
| title_full | Ksak: A high-throughput tool for alignment-free phylogenetics |
| title_fullStr | Ksak: A high-throughput tool for alignment-free phylogenetics |
| title_full_unstemmed | Ksak: A high-throughput tool for alignment-free phylogenetics |
| title_short | Ksak: A high-throughput tool for alignment-free phylogenetics |
| title_sort | ksak a high throughput tool for alignment free phylogenetics |
| topic | k-mer phylogentic tree alignment free open source microbiome |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1050130/full |
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