HPTree: Reconstructing phylogenetic trees for ultra-large unaligned DNA sequences via NJ model and Hadoop

2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Pub Date : 2016-12-01 DOI:10.1109/BIBM.2016.7822492

Q. Zou, Shixiang Wan, Xiangxiang Zeng

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引用次数: 9

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/.

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HPTree:通过NJ模型和Hadoop重建超大未对齐DNA序列的系统发育树

构建超大序列的系统发育树。文件超过1GB)是相当困难的，特别是对于未对齐的DNA序列。对大量不同的DNA序列进行多序列比对是没有意义和不可行的。我们首先尝试对DNA序列进行聚类，并将它们分成若干个聚类。然后对每个簇进行排列，并并行进行系统发育分析。Hadoop是云计算中最流行的并行平台，它被用于这个过程。我们的软件工具HPTree可以在几个小时内处理>1GB的DNA序列文件或超过1,000,000个DNA序列。用户可以在云计算平台(例如:Amazon)或自己的集群进行大数据系统发育树重建。不需要超级机器或大内存。HPTree可以使关注群体进化或长共同基因的用户受益。16s rRNA)进化。该软件工具及其代码和数据集可在http://lab.malab.cn/soft/HPtree/上访问。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

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