{"title":"HPTree:通过NJ模型和Hadoop重建超大未对齐DNA序列的系统发育树","authors":"Q. Zou, Shixiang Wan, Xiangxiang Zeng","doi":"10.1109/BIBM.2016.7822492","DOIUrl":null,"url":null,"abstract":"Constructing phylogenetic tree for ultra-large sequences (eg. Files more than 1GB) is quite difficult, especially for the unaligned DNA sequences. It is meaningless and impracticable to do multiple sequence alignment for large diverse DNA sequences. We try to do clustering firstly for the mounts of DNA sequences, and divide them into several clusters. Then each cluster is aligned and phylogenetic analysed in parallel. Hadoop, which is the most popular parallel platform in cloud computing, is employed for this process. Our software tool HPTree can handle the >1GB DNA sequence file or more than 1,000,000 DNA sequences in few hours. Users could try HPTree in the cloud computing platform (eg. Amazon) or their own clusters for the big data phylogenetic tree reconstruction. No super machine or large memory is required. HPTree could benefit the users who focus on population evolution or long common genes (eg. 16s rRNA) evolution. The software tool along with its codes and datasets are accessible at http://lab.malab.cn/soft/HPtree/.","PeriodicalId":345384,"journal":{"name":"2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","volume":"318 1","pages":"0"},"PeriodicalIF":0.0000,"publicationDate":"2016-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"9","resultStr":"{\"title\":\"HPTree: Reconstructing phylogenetic trees for ultra-large unaligned DNA sequences via NJ model and Hadoop\",\"authors\":\"Q. Zou, Shixiang Wan, Xiangxiang Zeng\",\"doi\":\"10.1109/BIBM.2016.7822492\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Constructing phylogenetic tree for ultra-large sequences (eg. Files more than 1GB) is quite difficult, especially for the unaligned DNA sequences. It is meaningless and impracticable to do multiple sequence alignment for large diverse DNA sequences. We try to do clustering firstly for the mounts of DNA sequences, and divide them into several clusters. Then each cluster is aligned and phylogenetic analysed in parallel. Hadoop, which is the most popular parallel platform in cloud computing, is employed for this process. Our software tool HPTree can handle the >1GB DNA sequence file or more than 1,000,000 DNA sequences in few hours. Users could try HPTree in the cloud computing platform (eg. Amazon) or their own clusters for the big data phylogenetic tree reconstruction. No super machine or large memory is required. HPTree could benefit the users who focus on population evolution or long common genes (eg. 16s rRNA) evolution. The software tool along with its codes and datasets are accessible at http://lab.malab.cn/soft/HPtree/.\",\"PeriodicalId\":345384,\"journal\":{\"name\":\"2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)\",\"volume\":\"318 1\",\"pages\":\"0\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2016-12-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"9\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1109/BIBM.2016.7822492\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1109/BIBM.2016.7822492","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
HPTree: Reconstructing phylogenetic trees for ultra-large unaligned DNA sequences via NJ model and Hadoop
Constructing phylogenetic tree for ultra-large sequences (eg. Files more than 1GB) is quite difficult, especially for the unaligned DNA sequences. It is meaningless and impracticable to do multiple sequence alignment for large diverse DNA sequences. We try to do clustering firstly for the mounts of DNA sequences, and divide them into several clusters. Then each cluster is aligned and phylogenetic analysed in parallel. Hadoop, which is the most popular parallel platform in cloud computing, is employed for this process. Our software tool HPTree can handle the >1GB DNA sequence file or more than 1,000,000 DNA sequences in few hours. Users could try HPTree in the cloud computing platform (eg. Amazon) or their own clusters for the big data phylogenetic tree reconstruction. No super machine or large memory is required. HPTree could benefit the users who focus on population evolution or long common genes (eg. 16s rRNA) evolution. The software tool along with its codes and datasets are accessible at http://lab.malab.cn/soft/HPtree/.
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