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

Año:2016

Áreas de investigación

Datos

Descripción
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.
Internacional	Si
Nombre congreso	International Conference on Bioinformatics and Biomedicine
Tipo de participación	960
Lugar del congreso
Revisores	Si
ISBN o ISSN	978-1-5090-1611-2
DOI
Fecha inicio congreso	15/12/2016
Fecha fin congreso	18/12/2016
Desde la página	53
Hasta la página	58
Título de las actas	HPTree: Reconstructing phylogenetic trees for ultra-large unaligned DNA sequences via NJ model and Hadoop

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